Nikolic officially stepped into office on May 31, when he was sworn in at the Serbian parliament.
Croatian President Ivo Josipovic said earlier in the week that he would not go Nikolic's inauguration.
"I cannot attend that inauguration for the reasons I have already given," Josipovic told the press.
Relations between Croatia and Serbia are increasingly better and I would like to see the continuation of this trend of good relations, the Croatian president added.
In previous statements, Josipovic said further cooperation between Croatia and Serbia could not depend on the good political will of only one side, as partnership required the two sides.
"I have clearly said that the new Serbian President should show by action that he embraces the highest European values on which we want to build our bilateral relations. Unfortunately, the views he has advocated to date and which he has reiterated in his recent public addresses, including his statement about Vukovar having been a Serb town and denying genocide in Srebrenica, are far from the European values," the Croatian president said.
Slovenian President Danilo Tuerk and the Chairman of Bosnia and Herzegovina's Presidency, Bakir Izetbegovic, also said they would not attend Nikolic's inauguration.
Izetbegovic said Nikolic had personally phoned him to invite him to the inaugural ceremony.
He said that was a nice gesture, but that Nikolic had changed his rhetoric and would have to prove if he had changed his position as well.