''Who was in charge?'' is the question American officials persist in asking, as Jonathan Jay Pollard, the U.S. Navy analyst, comes to trial on charges of spying for Israel. Increasingly embarrassed, Israelis are asking the same question.

The implication is that the Pollard operation, far from being a ''rogue'' in the Israeli intelligence structure, was actually the product of high government decision. But, in Israel's case, that is the wrong question. The issue is not so much whether prime minister or Cabinet members knew of the operation but, even if they did, whether they had any control over it.

Security officials cultivate autonomy -- be their agency the CIA or Israel's Mossad. Since their activities are secret, so are most of their blunders. In last year's Greenpeace affair, the French provided a rare glimpse of security services running amok.

In Israel, the problem is particularly severe, if only because the obsession with security creates a national disposition to give the secret services an extremely wide berth.

Israel has never had a government united enough to exercise strong institutional authority over its security agencies. This was never truer than today, when the two parties of the ruling coalition are bitter enemies, and both are deeply divided within themselves.

An Israeli prime minister's first concern necessarily is to preserve his government. He must indulge his defense minister, usually his rival, who nominally oversees secret operations. The foreign minister, a weaker member, is often excluded from intelligence deliberations, whatever their impact on foreign affairs.

''It is a defective structure which invites accidents, misunderstandings and malfunctioning,'' wrote Yitzhak Rabin, now the minister of defense, in a memoir a decade ago.

The structure is one that security officials readily manipulate. They know how to play ministers against one another, to operate in the seams between areas of ministerial authority. The system's fragility immunizes them from attack and, when they are caught in excesses,protects them from punishment.

Rafi Eitan, in charge of the Pollard fiasco, was by no means disgraced by the damage done to Israel's relations with Washington. The Likud Party, with which he had close ties, took care of him, and he became the highly paid head of a state industrial firm.

The Pollard affair is one a series of known instances causing serious injury to Israel's foreign relations.

The most notable came in 1954, when, to create an appearance of instability and undermine American confidence in the Egyptians, Israeli military intelligence ordered its underground cells in Cairo to bomb American diplomatic installations.

When the Egyptians arrested a ring of Jewish agents, Israel protested angrily, but a public trial left no doubt about its culpability. Not only had the prime minister been kept in the dark. Even the minister of defense had been excluded. In widening ripples of recrimination and embarrassment, the government itself fell.

Thirteen years later, a trial in Paris produced the revelation in Tel Aviv with the revelation that the Mossad had conspired with French and Moroccan security services in the kidnapping and subsequent murder of a prominent Moroccan opposition leader. The incident became a factor in de Gaulle's arms embargo in the Six-Day War.

The Israeli military analyst Yoram Peri has written that, despite the damage done by those episodes, ''the political leadership never had time to study the weak institutional links and to grapple with basics. Rather, it endeavored to move on to the next item on the agenda and to restore the status quo.''

The dilemma of the Pollard case is not so much who was in charge but how accountable are Israel's security services. It is a dilemma every country faces. But Israel, because of to its deeply rooted factionalism, must cope with an especially severe form of it.

Milton Viorst is a Washington writer who specializes in the Middle East.