<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0304</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2012-02-07</periodOfReport>

    <dateOfOriginalSubmission>2012-02-09</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000874733</issuerCik>
        <issuerName>MEDIWARE INFORMATION SYSTEMS INC</issuerName>
        <issuerTradingSymbol>MEDW</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001113678</rptOwnerCik>
            <rptOwnerName>CONSTELLATION SOFTWARE INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1200 - 20 ADELAIDE ST. EAST</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>TORONTO</rptOwnerCity>
            <rptOwnerState>A6</rptOwnerState>
            <rptOwnerZipCode>M5C 2T6</rptOwnerZipCode>
            <rptOwnerStateDescription>ONTARIO, CANADA</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-02-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>42100</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.6411</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1254580</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2012-02-08</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>15000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.7597</value>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1239580</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>318632</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Mark Leonard</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">5,000 additional shares were sold on this day but were inadvertently ommitted in the original filing.</footnote>
        <footnote id="F2">The updated price reported in Column 4 is a weighted average price. The shares were sold in multiple transactions at prices ranging from $13.50 to $13.70. The reporting person undertakes to provide to the issuer, any holder of the issuer's stock, or the SEC, upon request, full information regarding the number of shares sold at each separate price within the range described above.</footnote>
        <footnote id="F3">The price reported in Column 4 is a weighted average price. The shares were sold in multiple transactions at prices ranging from $13.80 to $13.92. The reporting person undertakes to provide to the issuer, any holder of the issuer's stock, or the SEC, upon request, full information regarding the number of shares sold at each separate price within the range described above.</footnote>
        <footnote id="F4">5,000 additional shares were sold on February 7, 2012 but were inadvertently ommitted. These additional shares are now reflected in this updated amount outstanding</footnote>
        <footnote id="F5">Shares are held by Mark Leonard, who is the President of Constellation Software Inc. The reporting person disclaims beneficial ownership of any such securities, except to the extent of its pecuniary interest therein, if any, and this report shall not be deemed an admission that the reporting person is the beneficial owner of such securities for purposes of Section 16 or otherwise.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Constellation Software Inc. /s/ John Billowits, Chief Financial Officer</signatureName>
        <signatureDate>2012-02-14</signatureDate>
    </ownerSignature>
</ownershipDocument>
