The two parties are deadlocked over on a deal over sharing of seats following DMK's decision on Saturday to pull out its ministers from the UPA government over Congress attitude.
The meeting, in which another DMK leader SS Palanimanickam was also present, came after their talks with Sonia Gandhi last night failed to yield results.
Congress sources said there was no breakthrough during the talks amid reports that Gandhi was peeved with DMK's decision to pull out its ministers from the UPA government.
There was no word from either side about what transpired during the talks with Mukherjee, who has been acting as the main trouble-shooter following DMK's sudden move last Saturday.
Reports had it that Gandhi had conveyed to the DMK leaders her displeasure over that party's action which had come as a bolt from the blue for the Congress in the middle of the budget session of Parliament.
Congress sources claim that the brinkmanship in the DMK was out of internal problems in the organisation between Alagiri, having influence in south Tamil Nadu, and Deputy Chief Minister MK Stalin, whose stronghold is north Tamil Nadu.
Sources said that Mukherjee has already twice held telephonic talks with DMK supremo M Karunanidhi and a possibility of Prime Minister Manmohan Singh coming into the picture at the last minute to hammer out a solution is not ruled out.
The Congress is insisting on contesting 63 seats whereas the DMK was prepared to give 60, twelve more over the number Congress contested in the last elections. DMK was also not wiling to concede to Congress the choice of seats.
A section in the Congress believes that a way out would be found out sooner than latter with DMK itself realising the problems it could face by such an action.
Meanwhile, Congress MPs from Tamil Nadu also met Mukherjee today to apprise him of their concerns in the matter.
"Congress votes are the deciding votes in Tamil Nadu. Only the party which is with the Congress can win. So far the alliance is on. I wish it will continue," Congress MP JH Haroon told reporters outside Parliament House.