The economy ministry said in a statement on Tuesday that the offers of the two bidders, Greek state-owned power utility PPC and Chinese consortium CWE&CTGPC, were "unacceptable."
The Macedonian government took the decision to cancel the tender on September 14.
The second phase of the tender for the construction of the two hydropower plants on the Crna river ended on December 15, 2011 and since then the decision has been postponed several times.
The next tender procedure will be conducted by the environment ministry, the statement added.
The two plants will have a combined capacity of 526 megawatts. The winner of the tender will build Cebren and Galiste in a public-private partnership with Macedonian state-owned power producer ELEM and will then operate the plants under a concession arrangement.