Utpal Parrikar, son of former Defence Minister Late Manohar Parrikar, lost to the BJP's Atanasio Monserrate, popularly known as Babush, by a slim margin of 716 votes.
Speaking to NDTV, Mr Monserrate said he is not happy with the margin of his victory and claimed that many BJP supporters did not vote for him.
"I have told this to BJP leaders. They should watch out in the future. The state BJP unit did not send the right message to the people. I am in touch with all BJP leaders and I am with the BJP," he said.
"I am not satisfied with the result. Many hardcore BJP voters have voted for Utpal. That is the reason he could get that many votes," he told the NDTV.
Mr Monserrate said the BJP is sure to form the next government in Goa. "Pramod Sawant will be our Chief Minister," he said.
Asked if he thinks a section of BJP leaders campaigned against him, he said the party leadership failed to "properly convey" the message to the people.
Utpal Parrikar had contested the election as an Independent after the BJP fielded Mr Monserrate from Panaji, offering the BJP veteran's son a different constituency.
An engineer, Utpal Parrikar had said he is staking his political career on fighting against the BJP's candidate in Panaji, especially as his father built the party from the ground up in Goa and in particular, the Panaji constituency.
Manohar Parrikar, a three-time Chief Minister of Goa, had held the Panaji seat for 25 years. In the by-election after his death in 2019, his long-time rival Monserrate, who is an accused in a rape case, won as a Congress candidate. Mr Monserrate later switched to the BJP.
The Shiv Sena and Arvind Kejriwal's Aam Aadmi Party (AAP) had openly backed Mr Parrikar. Shiv Sena's Sanjay Raut had appealed to all non-BJP parties to not field a candidate against Utpal Parrikar as a "tribute" to his father.
The BJP has won 20 out of the 40 seats in Goa, just short of the majority mark of 21. Chief Minister Pramod Sawant has said three Independents who emerged winners have pledged support to the BJP. Regional party, Maharashtrawadi Gomantak Party, has also said its two legislators will extend support to the BJP.
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