He rejected the invitation, raising speculation that this was to show displeasure toward President Lee about the government's religious policies.
Instead, Ven. Unsan, the head of a smaller Buddhist order, Taego, participated in the meeting.
Media reports said Ven. Jigwan ``was not able to go'' to Cheong Wa Dae because of a long-time previous appointment, quoting some monks at the Jogye Temple in Seoul.
``We are really sorry that we didn't have Ven. Jigwan at this meeting,'' said Maeng Hyung-kyu, senior presidential secretary for political affairs. "But it is not true that he rejected the invitation out of discontent toward President Lee. That is just speculation.''
Since President Lee's inauguration in February last year, he has had uneasy relations with Buddhists.
The country's second-largest religion planned a nationwide anti-government rally last year following the search of the car of Ven. Jigwan by riot police in front of the Jogye Temple, triggering outrage from monks.
Buddhist leaders called on President Lee to offer an official apology over the incident and his alleged bias toward Christians. Lee later expressed regret and promised to take measures to embrace Buddhists.
During the meeting at Cheong Wa Dae, Lee called for help from religious circles to tide over the economic crisis and ease social conflict.
President Lee, a Christian, asked religious leaders to help the administration promote reconciliation and national harmony at a time when inter-Korean tension is rising due to North Korea's nuclear test.
Lee invited the leaders of the seven major religions in the country to the meeting to discuss deepening ideological conflicts following the suicide of former President Roh Moo-hyun, the presidential office said.
Participants were leaders from Protestantism, Buddhism, Catholicism, Confucianism, Won-Buddhism, Chondogyo and an association of smaller religious groups.