Micheline Calmy-Rey gave no indication when the visa section would be reopened in the capital, Islamabad.
Pakistan and Switzerland enjoy close relations, but since earlier this year the local media has reported that some employees at the embassy's visa section maltreated applicants, received money, and were even allegedly involved in human trafficking.
Calmy-Rey, after talks with her Pakistani counterpart Khursheed Kasuri, on Saturday told reporters that "Switzerland finds itself in a difficult situation ... as a result of abuse of visa procedure that has been discovered at the embassy," according to state-run news agency, the Associated Press of Pakistan.
It also quoted Calmy-Rey as saying that the "criminal activity" at the visa section had not only damaged her country's interest and goodwill but also represented an act against those people who wanted to go to Switzerland.
Kasuri suggested the two countries should continue cooperation with each other to avoid any such scandals in future.
Earlier, Calmy-Rey also called on Pakistani President General Pervez Musharraf and discussed with him a wide range of bilateral and multilateral issues, Pakistan's foreign ministry said in a statement.