Macedonia's foreign ministry said it was informed by the embassy late yesterday that employees were being called back to Belgrade for consultations.
No reason was initially given for the move, which is likely to strain relations between the Balkan neighbours.
Vucic later told reporters in Serbia that the decision was made based on "sufficient evidence of highly offensive intelligence activities against certain organs and institutions of Serbia."
"Our duty is that our people be prepared and ready. There will probably be some changes in our staff to protect the friendship between Serbians and Macedonians," he added.
Macedonian media reports suggested the move was linked to Skopje's alleged decision to back a potential new bid by Kosovo to join UNESCO, the UN cultural body.
Serbia rejects Kosovo's independence claim and fiercely opposes its attempts to join international organisations.
Kosovo's application to join UNESCO in 2015 did not win enough votes from members, and it has not yet reapplied ahead of a general conference in two months.
When asked if the embassy withdrawal was related to a UNESCO bid, Vucic did not answer directly but said relations with Skopje "must be based on mutual respect."
Macedonia's government, which came to power in late May, released a statement saying it was "developing friendly relations" with neighbouring countries.
"With regard to the vote on Kosovo's accession to UNESCO, the Macedonian government will take into account the positions of the majority of EU countries," the statement said.
"When there are sensitive issues between our neighbours," it added, the government follows "good neighbourly relations and the promotion of regional cooperation, neutrality and non-interference in disputes."
Macedonia's new leftwing Prime Minister Zoran Zaev has at times had tense relations with Serbia's leadership, but he appeared to meet on good terms with Vucic at a summit in July.
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