Last week the Shakers announced they were under embargo due to a short-term loan obtained until mid-January and Manchester claims the shortfall is merely a matter of timing rather than anything more severe.
"It's within our means and we're confident we can pay it back in the time allocated," he said.
"It's all gone on expenses. Cash is king and sometimes it's just a timing issue and with us it's a timing issue.
"It's a difficult time over Christmas. Just an example, we were due to play Sheffield United in January. That's got put back and it's a midweek game.
"We'll lose about 2,000 fans - that's £30,000. All these things can conspire against you over time but we've been through worse than this before and got through it and we'll do the same again."
Manchester is confident manager Kevin Blackwell will be able to return to the transfer market in the January window and, in the meantime, discussions are ongoing with the Football League over whether Bury can extend the stays of their six-player loan contingent while the embargo is in effect.
"That's something that we're discussing with the Football League at the moment," Manchester added.
"First of all you've got to find out if the players want to stay here, then you've got to establish will the parent clubs allow them to stay here?
"So there's all these things to be considered and then we can talk to the Football League and see what we can do."
- Sports & Recreation