Hi,
Got this reply from Microsoft support and my error has been resolved after modifying changes in bank statement import services as mentioned below:
Hello Muhammad Matloob,
Greetings!!
I have researched in our internal knowledge database and found the Issue 3247038MT940 Debit or Credit marks are considered the opposite as expected for an advanced bank reconciliation.
Microsoft has evaluated this issue, and has determined that this functionality is working as designed.
You should customize XSLT for any change. The suggestion for a parameter to control whether change to opposite should be done or not during import is a viable suggestion and should be logged as a product suggestion in MSCONNECT.
If you want more information please go through the below LCS link :
https://fix.lcs.dynamics.com/Issue/NotFixed?bugId=3247038&qc=954a89077923ebf35c5f3469f47d49cb39ffb2430147d060a254f190d8f74a63
Workaround
Disclaimer
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MT940XML-to-Reconciliation.xslt
<xsl:template name="GetCreditDebitIndicator">
<xsl:param name ="Direction" select ="''"/>
<!--Reverse Debit Credit-->
<xsl:choose>
<xsl:when test="$Direction='C' or $Direction='RC'">
<xsl:value-of select="'Debit'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="'Credit'"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
Changed to
<xsl:template name="GetCreditDebitIndicator">
<xsl:param name ="Direction" select ="''"/>
<!--No Reverse Debit Credit-->
<xsl:choose>
<xsl:when test="$Direction='C' or $Direction='RC'">
<xsl:value-of select="'Credit'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="'Debit'"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
After this change, I deactivated the Inbound service for MT940 import (System administration | Setup | Services and AIF | Inbound ports), went to Inbound transforms | Manage transforms and reloaded the changed XSLT (MT940XML-to-Reconciliation.xslt).

After activating the port and importing the account statement, I could verify the expected result; the credit amounts on file were imported as credit on the bank statement ""
Hope this helps the users over Dynamics Community.
Regards
Muhammad Matloob