Ronald Muwenda Mutebi II's kingdom was restored in 1993
Ugandan Prime Minister Apolo Nsibambi has apologised to MPs for the manner in which three officials from the kingdom of Buganda were arrested.
They were detained for a week despite a court order demanding their release before they were charged.
Their dramatic arrest for sedition has been criticised by human rights groups.
A BBC reporter says the government has lately been at loggerheads with the traditional kingdom of Buganda over a controversial land reform bill.
The Baganda are the largest ethnic group in Uganda and their Buganda Kingdom was restored with limited political powers by President Yoweri Museveni in 1993, after it has been disbanded in 1966, four years after independence.
The kingdom has since been demanding the return of its communal land, but the government wants to give the tenants who have been on the land for the past few decades rights to farm it.
Mr Nsibambi was speaking at the end of a five-hour debate in parliament after the speaker had been forced to recall the house, which has been in recess, when 100 MPs signed a petition asking for the issue to be discussed.
Both opposition and ruling party MPs condemned the violation of human rights and demanded that a motion be moved to that effect.
No motion was moved, but the prime minister said that the government should recognise its mistakes, and enter constructive negotiations with the kingdom.
The BBC's Joshua Mmali in the capital, Kampala, says the arrests of the Buganda Kingdom officials has caused a furore.
Despite a court order to release the suspects unconditionally after their arrest on 18 July and a weekend spent in prison, they were re-arrested and transferred to western Uganda.
They were then charged with inciting violence and attempting to obtain firearms to engage in terrorism.
Medard Lubega, one of the suspects now on bail, told the BBC they were held incommunicado during their time in detention.
"How can you hold someone for seven days in various detention centres subjecting someone to psychological torture and emotional stress... then charge me with sedition which I [supposedly] committed in Kampala and you've been allegedly investigating in western Uganda?" he asked.
Call for action
After the parliament session, the internal affairs minister reiterated the need for an apology.
"It's our duty as a government and as a people and as a country to ensure that when mistakes occur they are corrected," Ruhakana Rugunda told the BBC's Focus on Africa programme.
"We have a system and mechanisms that ensure that mistakes are corrected and that the rule of law prevails."
But opposition MP Erias Lukwago said an apology was not enough.
"There is no serious commitment from government that they are not going to repeat these mistakes again," he told the BBC.
"We wanted action to be taken against the perpetrators of this violation of human rights and those who violated the constitution."