The highly unusual spat between the chancellery and foreign ministry on one side and the BND foreign intelligence service on the other hand erupted when the latter on Wednesday released a report accusing Saudi Arabia of a destabilising shift in foreign policy.
"The until now cautious diplomatic stance of the older members of the leadership of the royal family is being replaced with an impulsive policy of intervention," it said.
In particular, the BND focused on the role of Deputy Crown Prince Mohammed bin Salman who holds the defence portfolio and other powerful posts.
The BND said he and his father King Salman, who acceded to power in January, appeared to want to establish themselves as the "leaders of the Arab world" by advancing a foreign policy agenda "with a strong military component as well as new regional alliances".
German government spokesman Steffen Seibert said Friday it was crucial that Berlin has a "coherent position" on the role of Saudi Arabia in the region.
"The assessments by the BND that were published do not reflect this coherent position," Seibert said.
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"Those who want progress on the pressing issues in the region -- and there are many -- need constructive relations with Saudi Arabia," he said.
"Those who say that do not deny that there can be differences of opinion and differences in our political systems. But Saudi Arabia is a very, very important factor in the region."
He highlighted Saudi Arabia's participation in meetings in Vienna aimed at finding a political solution in Syria and plans to host a meeting of opponents of Syrian President Bashar al-Assad.
Foreign ministry spokesman Martin Schaefer insisted that Berlin had a "good and trusting" relationship with the BND in the analysis of the Middle East.
But he said the role of the BND, which reports to the chancellery, was to provide "information that the government requests" and "not to supply journalists with information".
Mohammed bin Salman has largely spearheaded Riyadh's handling of the war in Yemen, where Saudi Arabia is leading a coalition supporting the government against Iran-backed Shiite Huthi rebels.
Rights groups have repeatedly criticised the strikes, saying they have hit areas where there are no military targets.
Nearly 5,000 people have been killed in the war, more than half of them civilians, according to UN estimates.