The arrests were made in several villages around the capital, Skopje, police said.
Police found weapons, explosive devices, radio transmitters and uniforms of the ethnic Albanian guerrilla group the Kosovo Liberation Army which rebelled against Serb rule in 1998-1999.
The charging of the five suspects, the police raids and arrests were carried out in connection with the killing on 12 April of four Macedonian youths, aged between 18 and 22 and a middle aged man who were fishing at a lake near Skopje.
Of the five suspects charged with terrorism, three were ordered to be detained for 30 days while two others were still on the run, police said.
Macedonia’s state prosecutor Ljupco Svrgovski told media he would demand a maximum life imprisonment term for the five suspects if they are convicted.
Police minister Gordana Jankulovska told media the April murders were carried out in an effort to destabilize the small multi-ethnic Balkan country.
Ethnic Albanians make about 25 per cent of Macedonia’s two million population and mostly inhabit the western part of the country and the area around Skopje.
Ethnic Albanians rebelled in 2001, demanding more rights and regional autonomy, but the conflict was resolved through international mediation with the Skopje government agreeing to most of the ethnic Albanian demands.
Ethnic Albanian extremists in Macedonia have stepped up their activities in recent years, encouraged by Kosovo Albanians' secession from from Serbia in 2008.
Serbia opposes Kosovo independence, but it has been recognized by over eighty countries, including the United States and 22 out of 27 members of the European Union.