A fellow lawmaker said that the speaker of parliament announced Wednesday that Tin Aye - a lieutenant general until he retired last year to make a successful run for the lower house - had given up his seat.
Khin Shwe, an upper house lawmaker from the military-backed United Solidarity and Development Party, to which Tin Aye also belonged, said no reason was given.
Tin Aye has been the sixth-ranking member of Myanmar's junta, officially known as the State Peace and Development Council.
The future role of the junta under the new elected but still military-dominated government remains unclear. President-elect Thein Sein and Vice President Tin Aung Myint Oo, who are numbers four and five in the junta, remain members of parliament.
The military, which has ruled Myanmar since 1962, is notoriously secretive about its actions. Even under the new, nominally democratic government, which follows a general election last year, the proceedings of parliament are closed.
Parliament unanimously approved all the president-elect's 30 Cabinet nominees on Friday. It is not clear when he and his Cabinet will be sworn in.
Most of the Cabinet appointees are former military officers who retired to run in November's elections - the country's first in 20 years - and about a dozen were ministers in the junta's Cabinet. Only four of the appointees are strictly civilian.
Critics say the elections were orchestrated by the junta to perpetuate military rule. One quarter of the seats in parliament are filled by military appointees, and a large majority of the remaining seats were won by a military-backed party.
Nobel laureate Aung San Suu Kyi's party, which won the last elections in 1990 but was blocked from taking power by the military, boycotted November's vote, calling it unfair. Much of the international community also dismissed the elections as rigged in favor of the junta.