A number of Hearts' top earners were left awaiting their wages, which had been due on Monday, as last season's problems of paying salaries on time returned.
Press Association Sport understands the matter remained unresolved at close of business on Monday.
A statement on Hearts' official website read: "Hearts today confirmed that the vast majority of its 45-man squad had been paid their salaries in full.
"A small number of senior players were unpaid but will be paid shortly. The club has informed the affected players."
Hearts enjoyed a glamour UEFA Europa League tie with Liverpool last month but it, like all the other Scottish Premier League clubs, is awaiting the latest instalment of television revenue amounting to £300,000 ($465,317) per club.
A Hearts spokesperson added: "We have apologised to the small number of players affected by this short-term delay to their wage payments and we are grateful for their understanding on the matter.
"We expect the matter to be resolved once we receive a guaranteed income expected in the very near future."
Last season, three straight months of delayed player wages prompted an official complaint from the players, via union PFA Scotland, to the Scottish Premier League, but action was averted in January after Hearts met the demands imposed.
However, the issue reared its ugly head again in March, when players and staff received their salaries 12 days late.
Hearts attributed some of last term's delays to logistics transferring the funds from Lithuania, where majority shareholder Vladimir Romanov is based.