Demonstrators are angry with a proposed "compromise solution" that would allow North Macedonia to begin EU membership talks.
Police in North Macedonia say 47 officers were injured during a protest against a compromise on joining the European Union.
Thousands of people have demonstrated nightly in Skopje since the weekend over a French proposal aimed at lifting Bulgarian objections to North Macedonia's accession.
The injuries occurred after a group of mostly young people broke off from the main protest, throwing stones, metal bars, eggs and Molotov cocktails at the parliament building.
Prime Minister Dimitar Kovačevski condemned the attacks on the police, stating that violence cannot be justified.
Police also said that 11 protesters were detained on Tuesday after the clashes.
North Macedonia's Interior Minister Oliver Spasovski -- who visited the injured police officers in hospital -- confirmed that an investigation is underway.
“We all know very well who is behind the protests and who called for them,” Spasovski said, adding that the culprits would face the “strictest possible punishments.”
Thousands marched through the capital for a fifth consecutive night on Wednesday, where limited violence broke out.
A group of people threw stones, chairs and bottles at the protesters, while a 40-year-old man was detained after firing a gun in the air. No injuries were reported.
Bulgaria, which as an EU member has veto powers over new members, wants North Macedonia to formally recognise that its language has Bulgarian roots.
Sofia has also called on Skopje to recognise a Bulgarian minority in the country and to take further steps to quash “hate speech” against Bulgaria.
Many in North Macedonia -- including the main opposition party VMRO-DPMNE -- say acquiescing to these demands would undermine their national identity and favours Bulgaria.
North Macedonia’s president, Stevo Pendarovski, and the government has back the proposed French deal, which includes constitutionally acknowledging the existence of an ethnic Bulgarian minority.
MPs are set to meet on Thursday to set up a committee to examine the proposal.
North Macedonia has been a candidate for EU membership for 17 years. The country received a green light in 2020 to begin accession talks, but no date for the start of the negotiations has been set.
European Council President Charles Michel urged North Macedonia on Tuesday to back a French-proposed "compromise solution".
At a joint news conference, Michel stressed that the proposal is too “important an opportunity to be missed" and could lead to accession talks within days.