He was 71 and survived by his wife Uma Thomas and two children.
According to sources, Thomas died at 10.15 AM while he was undergoing treatment for cancer at Christian Medical College in Vellore.
P T Thomas, who was elected as MLA from Thrikkakara Assembly seat in April this year for the second consecutive term, represented Idukki in Lok Sabha during 2009-2014.
He also represented Thodupuzha Assembly constituency in Idukki district twice.
Born in 1950, Thomas began his political career as a worker of the Kerala Students Union (KSU), the student outfit of the Congress in Kerala, during his school days.
He held several positions, including state president of the KSU and Youth Congress during his eventful political career.
Kerala Governor Arif Mohamed Khan, Chief Minister Pinarayi Vijayan, Leader of the Opposition V D Satheesan, Congress national leaders Rahul Gandhi, K C Venugopal and Jairam Ramesh condoled the demise of Thomas.
"As a vibrant and dedicated legislator and parliamentarian, Shri #PTThomas had endeared himself to the people", Khan tweeted. He said Thomas was also noted for his fearless support to the protection of the environment.
Chief Minister Vijayan said the state has lost a noted parliamentarian through his demise.