CIA director Leon Panetta. — Photo by AP

ISLAMABAD: Four weeks into the Raymond Davis affair, an ongoing and very public spat between the ISI and the CIA threatens to engulf the fraught relationship between Washington and Islamabad. Partners in the war on militancy, the two spy agencies have never had an easy relationship. But ties hit a new low after the revelation that Davis was part of a clandestine CIA network operating in Pakistani cities.

“We feel betrayed by the CIA operations behind our back,” said an ISI official, speaking on the condition of anonymity.

ISI officials claim more than 50 CIA agents are still active in the country and are involved in intensive intelligence gathering without the knowledge of the ISI. “The Davis affair is just a tip of the iceberg,” commented one senor official.

The tensions were further set to escalate in recent days when the ISI prepared a statement — held back from publication at the last moment — in which the agency accused the CIA of being ‘arrogant’ and not showing ‘respect to the host country’.

The unprecedented riposte was meant to counter a comment made by an unidentified CIA official to an American newspaper that the ISI had suspended its cooperation.

However, repeated telephone contacts between CIA chief Leon Panetta and his Pakistani counterpart, Gen Ahmad Shuja Pasha, in the past week helped prevent a complete breakdown in the relationship.

The meeting last week in Oman between General Kayani and the top US military leadership also helped lower tensions. Although the Oman meeting had been long planned to review the situation in Afghanistan, discussions also focused on the fallout of the detention of the CIA contractor on the relations between the two allies.

According to some high-level sources, the meeting showed the determination of both sides not to let the Davis affair bring down the strategic ties between the two countries. “Sanity has prevailed,” claimed an ISI official.

Relations between the ISI and the CIA, rebuilt after 9/11, have been close in some areas, but a deep mistrust on both sides has remained. “It was a dysfunctional marriage at best,” conceded a Pakistani official.

In recent months, the tensions had once again escalated. A summons issued against Gen Pasha to appear in a New York court in connection with a private lawsuit centring on the Mumbai attacks was followed by the unmasking of the identity of the CIA station chief in Islamabad, forcing him to leave Pakistan.

But even before, for at least the past couple of years, some Pakistani newspapers have been publishing stories leaked by the ISI regarding the influx of US security contractors in large numbers. “They have to dismantle those networks if they really want our cooperation,” said an ISI official. “We have warned them that they cannot do things behind our backs.”

At present, there are some indications Washington is increasingly looking towards the Pakistani military leadership to help resolve the Davis affair. A possible reason is a feeling in Washington that the civilian government here is too weak and unpopular to deliver on the Davis issue.

Further complicating the issue, however, are the divergences between the civil and military leaderships in Pakistan. The military and the ISI now publicly criticise the civilian government’s decision to relax visa policies, a move that has led, according to the military, to scores of undercover US intelligence officials entering the country.

An ISI official claimed that 400 visa applications were processed by Pakistan’s embassy in Washington over a single weekend after the government on July 14, 2010, removed the requirement for intelligence vetting.

But some senior government officials privately blame the ISI for trying to instigate public opinion on the Davis issue.

The multiple power centres in the country has been a major reason for the Davis affair becoming a politically volatile issue, making it more difficult to find a diplomatic solution.

After an initial tough position, the Obama administration seemed willing to step back and negotiate an out of court settlement that would have included a public apology for the incident, the promise of a criminal investigation into the killings under US laws and the payment of compensation to the families of the victims.

But now, four weeks into the crisis, a resolution appears as distant as ever. Privately American diplomats believe it may take months for the Davis issue to be resolved.

“And it will take years to repair the damage the issue has done to Pak-US relations,” said an American diplomat.