The meeting assumes significance as the President will be holding talks with his Bangladesh counterpart Abdul Hamid, who arrived here on a six-day visit.
Banerjee, who is in the national capital and has been accusing the NDA government for making attempts to destabilise her government, is believed to have conveyed her stand on the Land Boundary Agreement (LBA) with Bangladesh.
The decision to implement LBA was taken by the previous UPA government headed by Manmohan Singh and his Bangladeshi counterpart Sheikh Hasina in September 2011.
During his visit to Assam last month, Prime Minister Narendra Modi had said his government will go ahead with the land-swap deal with Bangladesh for a permanent solution to the infiltration problem.
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Though Banerjee has been opposing the LBA on the face of it but West Bengal stands benefited from the agreement by getting more land whereas Assam will be losing some land.
In a related development, Foreign Secretary Sujtha Singh also met the President and briefed him on Indo-Bangla relations.
Mukherjee will hold discussions with his visiting Bangladeshi counterpart.
Meanwhile, doctors attending Mukherjee, who had paid a state visit to Bangladesh in March 2013, will review his health condition tomorrow morning after which a call on his discharge from the hospital will be taken.
When contacted, Press Secretary Venu Rajamony said "As of now everything including the banquet for the visiting dignitary stands as per schedule."
79-year-old Mukherjee is admitted to the Army Research and Referral Hospital since last weekend as he underwent a angioplasty.