Mukherjee told Nailatikau there was a need for an expansion of bilateral trade and investment between the two countries.
The Fijian President is on a private visit to India as he had stopped over in Delhi on his way back to Fiji after attending London Olympics.
During the meeting, Mukherjee recollected close historical relations between the two countries as well as presence of a large number of persons of Indian origin in Fiji, according to President's Press Secretary Venu Rajamony.
The Indian Cultural Centre in Suva, set up in August 1972, is India's oldest cultural center abroad.
Referring to the assistance provided to Fiji by India in the agriculture and sugar sectors, Mukherjee expressed happiness that India's development experience was being shared with Fiji through provision of training slots for their nationals and scholarships for students.
He also referred to assistance being provided in the health sector as well as cooperation in the defence field.
Fiji recently joined the Non-Alignment Movement, a step welcomed by Mukherjee, Rajamony said, adding the President also thanked Fiji for its support for reform of the UN Security Council as well as multilateral financial institutions.
Nailatikau conveyed his greetings to Mukherjee for being elected as the President of India and said Fiji was beneficiary of India's gracious assistance especially in the field of agriculture.
"Fiji has much to learn from India. The cultural centre in Suva has added tradition and colour to the fabric of Fiji society," according to Nailatikau.
He also extended an invitation to Mukherjee to visit Fiji.
Relations between India and Fiji date back to 1879 when Indian labourers were brought to the Pacific ocean island under indenture system to work on sugarcane plantations. Between 1879 and 1916 around 60,000 came to Fiji.
At least 37 per cent of Fiji's 8,49,000 population are people of Indian origin.
