Angus Robertson was accused of seeking "electoral advantage" in the independence referendum instead of sticking to a policy that was right morally.
Robertson, who is backed by First Minister Alex Salmond, is trying to persuade the party to drop its 30-year-old opposition to Nato membership in a vote at the annual conference in October.
The change is designed to ease voter concerns, and neutralise Unionist criticism, that an independent Scotland would be left unprotected.
Martin Sime, chief executive of the Scottish Council for Voluntary Organisations (SCVO), who has been accused of acting as a front for the SNP in the independence debate, took the trips in 2008 and 2009.
The Government gave the grant to the SCVO for "qualitative research on the relationship between civil society and governments in a range of countries", enabling Mr Sime to visit India, Australia, Africa and the US.
The organisation confirmed the money was used to pay for Mr Sime's travel and accommodation.