The election of the new secretary and its state committee is the last in the agenda of the 22nd State Party Conference that comes to a close with a massive public rally here on Sunday.
The 64-year-old leader was the former State Home Minister during 2006-11 in the VS Achuthanandan government.
An 87-member state committee was elected which saw nine existing members being left out and another 10 added.
Mr Balakrishnan told reporters that veterans like VS Achuthanandan and former ministers Paloly Mohammed Kutty and PK Gurudasan besides KN Rabindranath and MM Lawerence have all been included as special invitees to the state committee.
In January when a letter from a Middle East Arab businessman found its way to the party national leadership and to the media about the alleged financial dealings of Balakrishnan's elder son Bijoy, it had caused severe hiccups in the party.
While the issue was reaching a crescendo, reports surfaced that his younger son Binoy too had few cases in Dubai.
However, things turned out to be smooth for Mr Balakrishnan when reports surfaced that all issues had been cleared and the travel ban for Bijoy, preventing him to move out of Dubai, was also lifted.
"During the 2015 state conference, we ensured that factionalism at the highest level was rooted out and after three years, this time we concentrated to see that no such factionalism is there at the 14 districts and today at the end of the Thrissur conference, we have been successful to end factionalism here also."
He added that the upcoming assembly by-election at Chengannur and the general elections to be held next year are going to be their most keenly awaited events.
The state conference also decided to build 2,000 new houses for the poor and down trodden.
"The state conference has not come to any decision to reshuffle the state cabinet. Also when it comes to inducting new members to the state committee, it is a practise to leave out some due to age factor," said Mr Balakrishnan.
He also reiterated the decision of the 21st party Congress that there will be no tie up with the Congress.
"The BJP is the prime enemy and at the same time there will be no tie up with the Congress at all. The draft political resolution which will come up at the 22nd party Congress in April also states that there will be no such tie up," added Mr Balakrishnan.