The European Union had criticised Vladimir Leposavic for comments made last week about the massacre.
ADVERTISEMENTMontenegro's justice minister has denied accusations that made comments casting doubt on the events of the Srebrenica massacre.
Vladimir Leposavic said in parliament last week that he would recognise the massacre as genocide "when it is established unequivocally".
He said that the UN war crimes tribunal in The Hague did not have legitimacy because as, he alleged, it had got rid of evidence on the trafficking of Serb civilians' organs in Kosovo.
His comments sparked sharp criticism from the European Union, which urged the Montenegrin government to treat the victims of Srebrenica "with the utmost respect and dignity".
But in a statement on Monday, Leposavic said that his comments had been taken out of context.
"None of the above is true," he stated, "neither personally nor as a public official have I denied the crime of genocide in Srebrenica."
"I also made it clear that I do not dispute the legal obligation of decisions of international organisations and courts."
Several embassies in Podgorica had denounced the reported stance of the minister - who is considered to be pro-Serbian - and called on the Montenegrin authorities to condemn it.
But Leposavic said that his comments were meant to express his feelings towards equality.
"Distorting my words and manipulating them, proves only the intention of those who do it," said Leposavic.
"Before coming to office, I publicly spoke out and defended the rights of all national and religious communities against hate speech and discrimination, which I will continue to do in the future."
"I am sorry that I did not do so in a way that did not hurt any of my fellow citizens of the Islamic faith," he added.
At the end of the Bosnian war, 8,000 Muslim men and boys were massacred in July 1995 at Srebrenica, which is considered one of the worst atrocities in Europe since World War II.
The killings have been classified as genocide by the International Criminal Tribunal for the former Yugoslavia.
On the 25th anniversary of the massacre, world leaders urged governments to reject any denial of the genocide and demanded that Serbian leaders fully accept responsibility.
On Monday, EU spokeswoman Ana Pisonero rejected any attempts to relativise or misinterpret Srebrenica.
"It is high time for all political leaders in the region to lead the way in honouring victims and promoting reconciliation," Pisonero tweeted.
"Any country aspiring to join the EU is expected to comply with and promote EU values of democracy, human rights, tolerance and justice."
ADVERTISEMENT"This includes treating victims of genocide with utmost respect and dignity," she added.
Montenegro joined NATO in 2007 and began negotiations with Brussels in 2012, with a view to European Union membership.
In a statement, Montenegro's Prime Minister Zdravko Krivokapić said his cabinet did not want to "change the genocide" ruling of the UN war crimes tribunal in The Hague but rejected collective responsibility for the crimes.
Montenegro's government has stated it condemns "all war crimes" committed during the conflicts that marked the break-up of the former Yugoslavia.
"The government ... respects the continuity of international obligations of Montenegro, as well as the decisions of all international institutions," it said in a statement.
ADVERTISEMENT"The Montenegrin government neither wants to nor can change the decisions of international courts. We also cannot and do not want to declare some nations genocidal and others holy."