"I have to say I agree. Whatever the domestic political environment, this boycott is extremely unfortunate," Omar wrote on Twitter.
Omar was responding to a tweet by a user, who said the boycott was "extremely disturbing" and "sets a bad and irresponsible precedent".
Congress leaders, including party chief Sonia Gandhi and former Prime Minister Manmohan Singh, on Wednesday stayed away from a dinner hosted by Modi for African leaders, apparently sending a message that the party was outraged over an "insult" to the legacy of Jawaharlal Nehru.