While CPI-M General Secretary Sitaram Yechury told the media in Delhi that he was not aware of the case, the party's Politburo member Brinda Karat said the party had nothing to do with the case.
"This has nothing to do with the party and it will not interfere with it. This has to be dealt by the person himself and the party will not protect anyone," said Karat.
In her FIR, a 33-year-old Mumbai-based woman, who hails from Bihar, has alleged that Binoy sexually exploited her for several years on the promise of marriage. She decided to register a complaint at Andheri's Oshiwara police station on June 13, after she came to know that he was already married.
According to her complaint, she entered into a relationship with Binoy while working at a dance bar in Dubai in 2008 and now has an eight-year-old daughter with him.
However, Binoy has denied any wrong doing. He admitted knowing the woman but said that she was blackmailing him. He has also registered a complaint with the police against her.
"Six months back, I got a letter from her asking me to pay her Rs 5 crore. Following that, I filed a complaint with the IG of Police in Kannur.
"With regard to her allegation of the child, there are ways to scientifically ascertain parentage and I am ready for it," said Binoy.
Binoy and his brother Bineesh have been in the news since last year, when cases of financial fraud were registered against them in Dubai.
The rape case is a new headache for Balakrishnan and it comes at a time when his party is still smarting under one of its worst electoral reverses. The CPI-M won just one out of the 20 seats in Kerala in the recent Lok Sabha elections.
( With inputs from IANS )