Speaking to TV channels, Thomas had said that Chacko was acting in an authoritarian manner and trying to finish him off in his Kuttanad seat.
The minister was addressing an Iftar gathering here organised by the Kerala and Lakshadweep wings of the Nationalist Congress Party and its youth wing Nationalist Youth Congress.
The exit of members in Kasaragod is attributed to PC Chacko ignoring their complaints about election.
The Independent MLA dismissed rumours that he will become a part of the Left Democratic Front by rejoining his parent party.
Lathika and NCP's Kerala Unit President P C Chacko held discussions in this regard on Sunday.
The post was earlier held by TP Peethambaran.
Chacko, who is an influential leader from Kerala, was elected to the Lok Sabha from Thrissur (1991), Mukundapuram (1996), Idukki (1998 ) and Thrissur (2009) constituencies.
Chacko, 74, one of the Congress's top faces and spokespersons, is a former MP from Thrissur in Kerala.
Chacko, who had a bitter relation with a section of the Congress's Delhi unit, submitted his resignation to party interim chief Sonia Gandhi.
He said the only point of consolation is that the UDF was able to win with a margin of 2,079 votes the Aroor seat in Alappuzha district, considered a 'citadel' of the CPM for the last 42 years.