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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2005-07-20</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000737207</issuerCik>
        <issuerName>NASTECH PHARMACEUTICAL CO INC</issuerName>
        <issuerTradingSymbol>NSTK</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001195983</rptOwnerCik>
            <rptOwnerName>WENIG DEVIN</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3450 MONTE VILLA PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOTHELL</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98021</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Nastech Pharmaceutical Company Inc Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2005-07-20</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>4500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>369487</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Nastech Pharmaceutical Company Inc Stock Options</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>14.72</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-07-20</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>4500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.72</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-07-20</value>
            </exerciseDate>
            <expirationDate>
                <value>2015-07-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">N/A - restricted shares award</footnote>
        <footnote id="F2">Excludes 166 shares indirectly beneficially owned by the reporting person which shares are held by the reporting person's spouse.</footnote>
    </footnotes>

    <remarks>On July 20, 2005, the reporting person was granted (i) 4,500 restricted shares of common stock pursuant to the 2004 Stock Incentive Plan of Nastech Pharmaceutical Company Inc., and (ii) options to purchase 4,500 shares of common stock pursuant to the 2000 Stock Option Plan of Nastech Pharmaceutical Company Inc.  The restricted shares and the options vest in one year on July 20, 2006.</remarks>

    <ownerSignature>
        <signatureName>/s/ Gregory L. Weaver

Gregory L. Weaver
Attorney in Fact</signatureName>
        <signatureDate>2005-07-22</signatureDate>
    </ownerSignature>
</ownershipDocument>
