More than 1,100 servicemen and women from the Royal Scots Borderers and Highlanders are currently stationed outside Scotland.
But new figures suggest only a fraction of them are registered to vote on September 19.
Former Scottish Secretary Jim Murphy called on ministers to urgently contact all servicemen and women.
He said: "Scots who move abroad don't have a vote, but those in our Armed Forces are ordered abroad.
"They don't choose to move and they should not be excluded from the biggest decision of our history.
"That is wrong, and it has to change.
"It is time for the SNP government to act."