Speaking to reporters after visiting refugees from Croatia at the Krnjaca centre near Belgrade, Ljajic said SCG wanted good relations with Croatia because the European Union would not accept countries in conflict.
He also said that Croatia's 1995 military Operation Storm was ethnic cleansing because about 250,000 Serbs were expelled from Croatia.
Ljajic appealed to politicians in Croatia and SCG to refrain from "harsh words and big threats" and turn instead to dialogue to resolve the refugee issue.
He said he did not expect Croatian President Stjepan Mesic and Prime Minister Ivo Sanader to change their positions on Operation Storm, but added Serbia could not wait for that to happen so that the political climate could change to facilitate a successful refugee return.
Ljajic also said he felt Croatia was not fully ready to intensify the return process, adding that only 1,900 people had returned to Croatia in this year's first six months.
He said the return was not facilitated by the arrests of returnees in the last few months based on secret lists and indictments. He added Belgrade had still not received a revised list of Serbs accused of crimes in Croatia.