Thousands took to the streets of the capital Skopje demanding the resignation of President Gjorge Ivanov.
Some smashed windows and set fire to furniture at his offices.
On Tuesday Mr Ivanov gave 56 government and opposition figures, including former Prime Minister Nikola Gruevski, a blanket amnesty.
The scandal began when opposition leader Zoran Zaev accused Mr Gruevski of wiretapping about 20,000 people, including politicians and journalists.
They appear to show ministers plotting vote-rigging and even the cover-up of a murder.
Mr Zaev, who was also pardoned, said the president's move was illegal.
The government denies the allegations and accuses Mr Zaev of trying to "destabilise" the Balkan nation.
Twelve people were arrested in the second day of demonstrations and a journalist was injured, police said.
President Ivanov said he had acted in the national interest to "put an end to the agony" ahead of early elections in June.
Protesters enraged by the Macedonian president's pardoning of top political figures involved in a wire-tapping scandal have ransacked his office.