The two countries, both with majority Sunni Muslim populations, are bound together by shared Islamic religious ties, financial aid from oil-rich Saudi and Pakistani military assistance to the kingdom.
But a Taliban massacre at a school that killed more than 150 people in December, mostly children, has led the government to crack down on militants and talk of bringing religious seminaries under tighter control.
Now the country's media and even government ministers have begun to question whether support from Saudi Arabia for seminaries, known as madrassas, is fuelling violent extremism -- bringing tension to the relationship for the first time.
The Pakistani foreign ministry responded by saying that funding by private individuals through "informal channels" would also be scrutinised closely to try to choke off funding for terror groups.
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While the statement avoided mentioning Saudi Arabia specifically, it was widely interpreted as a rebuke.
Away from the seminaries, there has also been widespread criticism of the decision to allow Saudi royals to hunt the rare houbara bustard, prized in the Middle East for its supposed aphrodisiac properties, in the southern provinces of Sindh and Baluchistan.
Badar Alam, editor of Herald magazine, a respected Pakistani current affairs monthly, said the recent wave of criticism was unprecedented.
"Saudi has vast commercial and economic interests in Pakistan. There are open questions being asked on this relationship," he said.
"Before, nobody would ask any questions in any manner. Now even the Urdu press is asking questions."
The cable cited the Taliban, Al-Qaeda and Pakistan's Sunni Muslim sectarian militants Lashkar-e-Jhangvi as examples of where funds were being channelled.
But Najmuddin Sheikh, a former foreign secretary and ambassador, said the December attack on an army school in Peshawar, which left 153 people dead including 134 children, had opened the door for criticism.
"This has been triggered by Peshawar and a strong feeling that much of the terrorism that is here is being financed by outside countries," he said.
But, he added, any efforts to cut back on foreign funding for extremist seminaries must go hand in hand with similar efforts at home.
He said this would include the state dropping its links with proxy groups that have historically been used by the military establishment to further strategic goals in Afghanistan and Indian-administered Kashmir.
"Our fund collection within Pakistan remains unimpeded. If you want more from abroad you need to do more at home," he said.