Minister in-charge of social welfare department Sabitri Mitra and minister for public works Subrata Saha are now ministers without portfolio.
Tourism minister Krishnendu Narayan Choudhury was also divested of his portfolio.
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Sabitri Mitra and Krishnendu Narayan Choudhury are from Malda where TMC candidates lost to Congress at Malda South and North.
Trinamool Congress won 34 seats out of 42 seats in the Lok Sabha polls.
The reshuffle, which came five months after a similar exercise in December last year, saw Banerjee alloting additional responsibility of Information and Technology department to Amit Mitra, who is now regarded as the key man in her Cabinet.
Mitra, a former director-general of FICCI already holds two key portfolios - Finance and Industry besides Public Enterprises and Industrial Reconstruction.
Partha Chatterjee, a political heavyweight in the party and Banerjee's close associate who held IT, was given the important Education portfolio to streamline the department. He will continue to look after the Parliamentary Affairs portfolio.
The state recently witnessed protests by student wings of the Left parties and Congress against alleged irregularities in the recruitment of primary teachers in state-run schools.
The actor and playwright-turned politician Bratya Basu who held the Education portfolio would now hold Tourism portfolio, which was taken away from Chowdhury.
Chowdhury, who is from Malda district, has been shifted to Food Processing and Horticulture department which was held by Subrata Saha.
Saha is TMC leader from Murshidabad district where too the party put up poor performance in the parliamentary polls.
He now remains a minister without portfolio.
Social Welfare has been given to Women and Child Development Minister Sashi Panja as additional charge.
Chowdhury, Mitra and Saha came under fire from Banerjee in a recent cabinet meeting.
Congress retained the two parliamentary seats in Malda-- Malda North and Malda South-- and the Behrampore seat in Murshidabad.
TMC finished third in Malda North and a poor fourth in Malda South. In Behrampore, TMC finished second.Both Chowdhury and Mitra, elected on Congress tickets from Malda in the 2011 Assembly polls, had switched loyalties to TMC.
Chowdhury got elected on a TMC ticket before the two were given ministerial berths by Banerjee in a bid to strengthen the party organisation in Malda district.
A senior party leader from Burdwan district, Malay Ghatak has already resigned as Agriculture minister apparently because Banerjee was unhappy with him for failing to ensure the victory of TMC candidate in Asansol Lok Sabha seat.
BJP's new entrant singer Babul Suprio won a maiden victory for the party.