Opposition leader Zoran Zaev blasted the move by President Gjorge Ivanov as illegal, and a few hundred people took to the streets of the capital Skopje in protest.
In a televised address to the nation, Ivanov said yesterday he was bringing the legal proceedings to a halt "in order to put an end to this political crisis, which will end with democratic elections".
Last year Zaev's Social Democratic Union of Macedonia (SDSM) accused then prime minister Nikola Gruevski of wiretapping around 20,000 people, including politicians and journalists, and said the recordings revealed high-level corruption.
A special prosecutor has been probing the wire-tapping scandal and all the allegations.
Gruevski - the former strongman leader who is a political ally of the president - was among those being targeted in the probes, along with Zaev, former interior minister Gordana Jankulovska and ex-intelligence chief Sasho Mijalkov.
The EU expressed alarm at the president's move.
"Today's decision by President Ivanov on the pardoning of a number of officials raises serious concerns," the bloc's foreign policy arm said in a statement.
EU Enlargement Commissioner Johannes Hahn said on Twitter that Ivanov's decision was "not in line with my understanding of the rule of law."
Hahn urged Macedonian political leaders to get back to the negotiating table, warning that recent political actions "put the Euro-Atlantic future of their country seriously at risk."
Macedonia has been a candidate for EU membership since 2005 but accession talks have yet to open.
Zaev said the pardons broke last year's EU-mediated political agreement to end the crisis, and urged protesters to take to the streets. A few hundred demonstrators gathered outside the prosecutor's office late yesterday.
"We have no doubt in his honest and good intentions... But we want to express our huge disagreement with his move," the party said in a statement.
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