Paul Martin, 36, was named with Michael Brown, the Conservative MP, in Sunday newspaper allegations of homosexual impropriety.
The MoD said Mr Martin, a junior official in the Nato and European Policy Secretariat, would remain suspended until the outcome of an investigation to determine whether national security had been placed at risk.
''He has not become deeply involved in any long-term projects,' a spokesman said. 'His job is basically drafting material for senior officials and ministers. He is not a major adviser.'
But the spokesman added Mr Martin had worked at the ministry for only a short time and was a middle grade civil servant.
The MoD told the Independent yesterday that Mr Martin would be questioned about the conduct of his personal life.
Mr Martin had been a young political high-flier. He was a Conservative councillor on Edinburgh council for 12 years and had been a former group leader.
He had also twice contested parliamentary seats. In 1983 Mr Martin fought the parliamentary seat of Edinburgh East and reduced the Labour majority by 6,000. In 1992, he unsuccessfully fought the parliamentary seat of Edinburgh Central.
Mr Brown, a Tory whip, resigned from the Government immediately after the allegations were published. He said that he wished to concentrate on taking legal action against the News of the World, which had linked him with a 20-year-old student at the London School of Economics.Reuse content