Mukherjee's summons came hours after Congress President Sonia Gandhi discussed the matter with senior party leaders and senior Union Ministers.
Tharoor is at the centre of a controversy over IPL team that was sold to Kochi last month for 1530 crores.
One of Tharoor's close associate Sunanda Pushkar, was gifted equity worth 70 crores by the team-owners.
On Monday, in a comment on social networking site twitter, the IPL commissioner Lalit Modi revealed details of Kochi team's stakes.
In Washington, the Prime Minister Manmohan Sigh who is on a week long visit to the US and Brazil, said he would take any action, if required, after he returned.
"I do not know the facts," said Manmohan Singh, adding that he could not go by what the media was reporting on the issue.
Meanwhile, in an interview to a private news channel Tharoor maintained that his party has not left him out in the cold and declined to resign from the Cabinet over the issue.
"Resigning would mean I've given up," Tharoor said.
Tharoor said he would convey details of his relationship with the Kochi IPL team to Sonia Gandhi and the Prime minister Singh.
"I have done nothing wrong, I stand with my head held high," he said.
The Income Tax Department is reportedly gearing up for a formal inquiry to check source of funds of Rendezvous Sports World, the group that bought the Kochi team.
The Bahratiya Janata Party (BJP) has demanded that the Prime Minister Singh to sack Tharoor for inappropriate "patronage and protection".
The BJP alleges that Pushkar was a front for Tharoor, and that the CBI must investigate Tharoor for "criminal misconduct by a public servant" in what it describes as "a copybook case of corruption."
The Left has joined in with a statement released on Wednesday in which the Communist Party of India- Marxist (CPM) said: "It is highly inappropriate for a minister in the Union government to be involved in such murky dealings...It is incumbent upon Mr Tharoor to step down from office till his name is cleared of any unethical or irregular behaviour." (ANI)