Sources said that the issue could not be resolved despite marathon deliberations and the leaders will again meet tomorrow.
The meeting was attended by former Karnataka Chief Minister Siddaramaiah, Deputy Chief Minister G Parameshwara, state party in-charge K C Venugopal, and senior leaders Mallikarjun Kharge and D K Shivakumar.
"We discussed about portfolio allocation. First, we need to finalise the portfolios between the two parties. Thereafter, we will decide whom to allocate what ministry," Venugopal told PTI after the meeting.
The entire process will be completed in a day or two, he added.
The Congress and the JD(S) are at loggerheads over the key portfolios of Finance and Home.
Chief Minister and JD(S) leader H D Kumaraswamy has admitted to having "some issues" with the Congress over portfolio allocation that was delaying the formation of the entire council of ministers.
On May 23, Mr Kumaraswamy and Mr Parameshwara took oath and chief minister and deputy chief minister respectively.
The issues of according adequate representation to various regions and maintaining the caste balance in the state are weighing heavy on both the parties.
It has already been decided that Congress would have 22 ministers and JD(S) 12 in the new council of ministers.
The sources said that the Congress will take a call initially on having 16-17 ministers.