Police spokesman Ivo Kotevski told the AP that the 60 were charged Wednesday with participating in a mob intending to cause a crime.
Sunday's clash between mainly Muslim ethnic Albanians and orthodox Christian Macedonians broke out at the historic Kale Fortress in a dispute over a new structure being built on the foundations of a 13th-century church. The ethnic Albanians object to what they said was the rebuilding of a church on the site and have demanded a mosque be built alongside it.
Minority ethnic Albanians staged a brief uprising against the government in 2001. Nearly 90 people were killed in the six-month conflict.