The first son of prominent Syrian Church reformist Abraham Malpan (the "Martin Luther of the East"), he was born into the Palakunnathu family of Maramon.
There was no proper Theological education for Clergy, Holy communion was conducted for money, the church buildings belonged to one or two respected families of the parish.
Palakkunathu Thomas Mar Athanasious initiated a large number of reforms at Church administration and at the parish level like his predecessor.
However, the opposition party Pulikkottil Joseph Mar Divaniyos II in 1876, brought the Patriarch of Antioch to preside over the Synod held at Mulanthuruthi.
To establish the foothold by the two factions, a litigation, that lasted for 10 years, took place regarding the title to the possession of the ‘Syrian Seminary’ and allied properties of the Church.
Though the episcopate of Thomas Mar Athanasius was a period of trial and suffering for the Church, it was also one of great spiritual promise for the future.