The message, written by the DWP's top civil servant Robert Devereux, was criticised for being "ill judged" amid concerns it could be seen as telling staff in Scotland how to vote in next month's independence referendum.
But the DWP insisted the memo was simply intended to set out for staff the restrictions of the purdah period in the run-up to the September 18 ballot.
The BBC reported the memo said: "It is important that, as civil servants, we understand why the Scottish independence referendum is different from elections such as a UK general election or a European election.
"This is because the UK Government has a clear position to maintain the union and so it is legitimate and necessary for UK civil servants to support the Government in this objective."
Dave Penman, general secretary of senior civil servants' union the FDA, said the memo was "ill judged" and added: "It is factually accurate but it probably could have been written a lot more sensitively."
A DWP spokesman said: "Of course the department has not told its staff, or anyone else, how to vote.
"It was an open letter to all DWP staff setting out Scottish referendum guidance and the role of the civil service.
"Similar advice has been issued by the Scottish Government."
Scottish First Minister Alex Salmond said unions are "furious" at the letter, insisting it amounts to apparently giving "an instruction to people on how to vote".
"I thought it was quite extraordinary," he told the Press Association at a press conference in North Berwick, East Lothian.
"The unions were furious, and rightly so because it is no part of what a government should be doing, the Westminster government apparently dictating to its employees.
"Now maybe it's just badly worded, maybe that's not what they meant to say. Well, if that is the case, they should withdraw the letter and apologise to their staff.
"It's not something the Scottish Government would ever do, give the impression that we've got the right to dictate to our employees. You don't have the right."
Mr Salmond's own top civil servant Sir Peter Housden has faced unionist accusations of "going native" for advancing the Scottish Government's policy of promoting independence.
The First Minister said it is the job of civil servants to promote the policies of the government of the day, but "that is not what that (DWP) letter suggested".
He said: "As far as the opposition attacks on civil servants, this phrase 'gone native', what exactly does that mean? That they have gone sticking up for Scotland, which is the job of everyone in Scotland never mind civil servants, never mind Scottish Government ministers.
"It's an entirely different thing from sending a letter, perhaps loosely phrased, perhaps worse than that, which the unions are so furious about, which apparently gave an instruction to people on how to vote."