On his first day in office, Moon Jae-In named Im Jong- Seok to be his chief of staff, the second most powerful position in a political system which concentrates authority in the president.
Im, a 51-year-old former two-term lawmaker with the Democratic Party, was a prominent student activist in the 1980s and, like Moon, protested against military rule.
Outspoken and charismatic, Im has long been dogged by accusations he is a North Korea sympathiser.
The two Koreas remain technically at war and under South Korean law its citizens need government permission to go to the North.
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Even though he did not go to Pyongyang himself, Im was convicted and jailed over the trip.
He eventually entered politics in 2000 as a lawmaker for the Democratic Party and was later a deputy mayor of Seoul.
Im vowed to create an "open" office compared to the secrecy that surrounded it under ousted leader Park Geun-Hye, and told reporters: "I will serve Moon with all my heart, but will not become a yes man."
"We can't help expressing regret over the nomination," it said in a statement, warning that it would further deepen concerns over Moon's stance on North Korea.