Prosecutors have since 2015 been investigating allegations of top-level corruption by the then conservative government led by VMRO-DPMNE leader Nikola Gruevski.
The accusations came from tapes that emerged as part of a major political scandal over revelations that authorities had wiretapped some 20,000 people including politicians and journalists.
Media reported that top VMRO-DPMNE officials were among those charged Thursday -- including Gruevski, who was prime minister from 2006 until 2016.
Prosecutors have charged 94 people and seven companies and institutions, special prosecutor Katica Janeva told reporters.
"Firm evidence was secured for serious abuse of institutions by individuals and organised groups, abuse of power and authority and violation of laws during public procurement procedures," Janeva said.
"It will be proved that the suspects were responsible for the acts."
Gruevski branded the charges as "classic political persecution".
"VMRO-DPMNE is being attacked as never before in Macedonia. This is a political and not a judicial process," Gruevski told reporters, adding that prosecutors have "no legal evidence".
After a snap vote prompted by the turmoil, Social Democrat leader Zaev took over as premier on June 1, in a first step towards ending the crisis.
The special prosecutors' office was set up in September 2015 as part of a deal between all political parties to overcome the scandal.
A court is set to decide on prosecutors' request that 18 of the officials be detained, on a date yet to be confirmed.
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