The East End Park boss also described the past six months at the cash-strapped club as the worst of his footballing career.
The Pars have just six days to come up with £134,000 or face being wound up after Her Majesty's Revenue and Customs took the 128-year-old club to court over an unpaid tax bill.
Dunfermline also understood to owe around £8million to directors past and present and have repeatedly failed to pay their players on time this season.
It was confirmed earlier this month that Jefferies' squad and other staff received just 20 per cent of their wages.
But the former Hearts boss claims he and his squad only discovered the true extent of the financial crisis two weeks ago.
He said: "Gavin Masterton has put a lot of money into Dunfermline. And there is no doubt he has done some good things.
"But he was dependant on a lot of things happening at the club.
"We as players and coaches just want to prepare properly and look after the football side.
"But you expect to get your salaries on time. The club can certainly be a wee bit late - that would have been okay with our players - but when it's gone on this long, there is a sense that we've been let down.
"A lot of the guys are dependant on that money and we didn't know how things were coming about.
"Gavin was trying to buy a bit of time but time ran out. The things he hoped would come off didn't and the up shot of that was that the players have been left with very little money coming in."
Earlier this month, majority shareholder Masterton announced he would walk away from the club and hand over his stake to supporters but talks with The Pars Community broke down amid acrimonious squabbles.
That has left another group - the Dunfermline Athletic Steering Group, led by ex-manager Jim Leishman - to try to raise the necessary cash needed to save the club.
But Jefferies believes the Steering Group is now being asked to tidy up the mistakes of the past.
He said: "This is probably the worst situation I've been in at a club.
"Dunfermline were at a stage a few years ago where they were able to spend decent money on trying to get success. They were in the top six of the SPL and in cup finals.
"But sometimes you just get carried away and start chasing it further and bring more players in. But like a lot of clubs have found, that will come home to roost.
"It's not managers' fault. They want to get what they can and if they get it, they will spend it on transfers or salaries.
"But it's down to people who run football clubs to say what they can spend and what they can't."
Dunfermline had started the season hoping to bounce straight back to the Clydesdale Bank Premier League after last term's relegation.
But despite mounting an early challenge for promotion from the Irn-Bru First Division, they have now find themselves 17 points adrift of leaders Morton.
Their lowest point came on March 2 when they were humiliated 4-0 at home by Partick Thistle and Jefferies admits the stress of the past few months has taken its toll on his players.
"Gavin was working hard and was promised some investment into the club through different routes," he said.
"He reassured everyone at the club when this all started that come the end of December, everything would be back on an even keel and everyone up to date with the money they were owed.
"But that didn't happen for various reasons.
"That led to frustration. When you are told 'it is coming, it is coming, it is coming', you can only go on so long.
"I said at the beginning that if it dragged on it would become a problem. We're into the fifth or sixth month now and that has happened.
"The players quite rightly became frustrated with the whole thing and the Partick game became the breaking point.
"But since then things have moved on. Gavin has understood that and it's forced him to move on.
"Everyone has now been explained to just what position the club was in. We didn't know that until a couple of weeks ago. But everybody knows where they stand now and the players have had to accept that.
"There has been a general change in the attitude. They know they are only hurting themselves by being frustrated. They have decided to get out there and use the football as an escape."