JERUSALEM — The corruption investigations closing in on Prime Minister Benjamin Netanyahu of Israel had caught up his wife, his personal lawyer, a former chief of staff and other close confidants — nearly all of them, it seemed, save one: Yitzhak Molho, the lifelong friend Mr. Netanyahu has relied upon to negotiate with the Palestinians, sent on secret diplomatic missions and turned to on sensitive matters since the 1990s.

So much for that.

The police confirmed on Tuesday that Mr. Molho, the 72-year-old managing partner of one of Jerusalem’s leading law firms and chairman of the Israel Museum, had been detained for questioning in perhaps the weightiest of the investigations underway: an expanding inquiry into the circumstances surrounding the multibillion-dollar purchase of three new submarines from a German shipbuilding company. Israeli news reports, citing unnamed sources, said Mr. Molho was suspected of a conflict of interest and breach of trust.

To some who have negotiated with him, Mr. Molho’s interrogation, disclosed after the expiration of a 48-hour court-imposed gag order, was baffling. “Hard to fathom,” Dennis B. Ross, the former United States Middle East envoy, wrote in an email. Saying he had worked closely with Mr. Molho for 20 years and found him “careful and meticulous and always ethical,” Mr. Ross added: “I doubt there is anything that actually touches him.”

But to critics of Mr. Netanyahu, Mr. Molho’s detention on Sunday along with that of David Shimron, a partner in his law firm who previously had been named as a suspect in the submarine investigation, highlighted a glaring, longstanding problem in the way the prime minister has run his government: The two men were perhaps his most trusted advisers, yet neither had given up private law practice — leading, at a minimum, to the appearance of a conflict of interest.