He signed the register only after officials and several MPs reminded him.
Gandhi has been elected to Parliament from Kerala's Wayanad. He had also contested from his family borough of Uttar Pradesh's Amethi but was defeated by BJP leader and Union Minister Smriti Irani by a margin of over 55,000 votes.
Gandhi took the oath in English this afternoon and began walking away towards his seat when he was reminded of the necessary signature. He then signed the register and walked back to applause from his party members including mother Sonia Gandhi.
Earlier in the day, his absence was recorded by the ruling party members, who asked where he was.
Soon after questions were raised over his absence on the first day of the Budget Session, Gandhi took to Twitter and wrote, "My fourth consecutive term as a Member of the Lok Sabha begins today. Representing Wayanad, Kerala, I begin my new innings in Parliament by taking my oath this afternoon, affirming that I will bear true faith and allegiance to the Constitution of India."
On the first two days of the session, the oaths are administered to the 542 lawmakers.
The process was started by President Ram Nath Kovind who administered the oath to Pro-tem Speaker Virendra Kumar, who in turn administered the oaths to the other lawmakers.
The Congress is yet to announce its leader in the House.
( With inputs from IANS )