The payment fell far short of the $11 billion (9.62 billion euros) in reparations demanded by Kinshasa over a conflict that is believed to have killed hundreds of thousands of people.
In 2005 the ICJ ruled that Uganda had to pay reparations, but the two countries never settled on an amount and no money changed hands.
Uganda's foreign ministry said it was "doing all in its means" to work with the DRC government in matters of security, infrastructure, and regional economic integration.
Uganda protested Thursday at an order by the UN's highest court for it to pay the Democratic Republic of Congo $325 million in damages over a brutal war two decades ago.
The payment fell far short of the $11 billion (9.62 billion euros) in reparations demanded by Kinshasa over a conflict that is believed to have killed hundreds of thousands of people.
"While the amount awarded is far less than that sought by the DRC, Uganda nevertheless considers the judgment unfair and wrong, just as the previous 2005 judgment on liability was unfair and wrong," Uganda's foreign ministry said in a statement.
"Uganda regrets that this decision comes at a time when the two countries are continuing to strengthen their relations."
Wednesday's ruling by the International Court of Justice was the culmination of a long legal battle between the neighbouring countries over the conflict.Â
In 2005 the ICJ ruled that Uganda had to pay reparations, but the two countries never settled on an amount and no money changed hands.
Kinshasa then claimed more than $11 billion for the occupation of its volatile northeastern Ituri region.
The court acknowledged that Uganda was to blame for a "significant part" of the casualties in the war due to its "wrongful international acts".
But judges said there was insufficient evidence to support the DRC's claim that Uganda was directly responsible for 180,000 civilian deaths.
Kampala questioned why Uganda was being singled out when it said the armies of eight countries were involved in the 1998-2003 war.
"For the record, Uganda disputes and rejects the findings of wrongdoing by the Uganda People's Defence Forces (UPDF), widely known as one of the most disciplined forces in the world," the ministry statement said.
It did not say whether Uganda would pay or not.
The Congolese and Ugandan armies launched a joint operation late last year against the Allied Democratic Forces armed group which is blamed for thousands of killings in the eastern DRC as well as recent bomb attacks in Uganda.
Uganda's foreign ministry said it was "doing all in its means" to work with the DRC government in matters of security, infrastructure, and regional economic integration.
"The problems that led to Uganda's presence in the DRC between 1998 and 2003 were not solved then and they are still not solved even now," it said.