He then urged his team to go on a cup run to help increase the chance of the situation improving.
The manager said only 65% of salaries went into the bank on Thursday as the Fife club continue to grapple with a severe cash-flow problem while owing money to Her Majesty's Revenue and Customs and ScottishPower.
Jefferies, whose team have lost their last two league games, knows a win against Hamilton today, followed by a plum tie in the quarter-finals, could make a considerable difference to their struggles. He said: "The stuff about the wages hasn't been the best preparation. It's not what you want to hear when you come in on a Thursday morning.
"But the boys have been professional throughout the season and they'll continue that. Hopefully, we can get the win that can help the club and the players financially.
"Both teams will be saying they have an opportunity to progress to the next round, but have the advantage because we're at home.
"Hopefully the crowd will get behind us because, as we've said to the players, with all the financial problems at the club, this is a way to try to get more money in. The further we go in the cup, the better chance we have of getting paid."
Billy Reid, the Hamilton manager, warned his squad there must be no repeat of the performance in last week's league defeat to Dumbarton, or they will find themselves out of the cup.
Reid said: "We played Dunfermline recently at East End Park and probably had the better chances in a 1-1 draw but there is very little between the teams.
"We cannot give them the advantage of getting on top early and having us chase the game. We will travel with confidence following our last display there, but we know we have to play well to get through."
Alex Neil is eligible to play, with his current three-game suspension applying only to league matches. Gary Fraser is also included after pulling out of a transfer to Bolton Wanderers in midweek, the 18-year-old deciding he did not want to move away home. Conner McGlinchey left Accies by mutual consent last week and knee injuries have ruled out Jon McShane and Kieran Millar.