Thein Sein told reporters in Tokyo the Nobel Peace prize winner would be welcomed into the chamber, but that taking the seat she won earlier this month was up to her.
"Ms Suu Kyi needs to decide whether she wants to enter parliament or not," Thein Sein said, when asked in a group interview in Tokyo about the possibility of revising the wording of a contentious oath, Kyodo reported.
"Myanmar`s parliament is all in favour of her entrance and very much welcoming her."
Suu Kyi`s party has refused to swear to "safeguard" an army-written constitution.
The president, who is on a five day visit to Japan that ends Tuesday, also affirmed that the process of democratisation in the country would not be reversed.
"There won`t be any U-turn," Thein Sein said. "We would like to cooperate (with Suu Kyi) by heading in the same direction, in the interest of the people," the Mainichi Shimbun reported.
Thein Sein also left open the door for Suu Kyi to enter government, but said she had to decide where her priorities lay.
Noting that the constitution does not allow lawmakers to become members of the cabinet, he said: "Suu Kyi has to make her own decision."
"Suu Kyi should work for the people, rather than her own party," Jiji press cited him as saying.
Asked about any change to the constitution, the president said: "It will be decided by the wishes of the people, the opinions of the people."
Thein Sein`s comments, on a visit to Japan that has seen Tokyo promise to forgive $3.7 billion of debt and restart aid programmes, were his first since Suu Kyi`s party threatened to boycott Monday`s opening parliamentary session.
The Nobel laureate, who spent much of the past two decades locked up by the former junta, had been set to make her debut in parliament after her party`s decisive win in by-elections earlier this month.
Suu Kyi`s National League for Democracy (NLD) -- the main opposition force after securing 43 of the 44 seats it contested in the by-elections -- has appealed to the president directly over the stalemate, asking that the wording of the oath be changed from "safeguard" to "respect" the constitution.
It is the first sign of serious discord between the NLD and the military-backed regime since the polls. (*)
Editor: Kunto Wibisono
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