Uganda summoned the European Union's envoy on Friday to explain his criticism of President Yoweri Museveni's handling of corruption.
The move underlined growing friction with the West after it cut aid over graft concerns.
Western donors withdrew almost all direct budget support to the east African nation after allegations that $13 million had been stolen by officials in the prime minister's office.
Roberto Ridolfi, head of the EU delegation, was quoted on Wednesday by the privately owned Daily Monitor newspaper as saying it was a "pity" that Museveni's recent state of the nation address had failed to address corruption, a crackdown on critical media and his own succession.
The EU delegation's office issued a statement confirming Ridolfi's remarks as carried by the newspaper but said they disagreed with the headline the paper had chosen, which read: "European Union diplomat attacks Museveni over graft."
"We have called him (the ambassador) because he needs to explain that Daily Monitor headline and the remarks attributed to him," Foreign Ministry permanent secretary James Mugume told Reuters.
"It's not acceptable. An ambassador is not supposed to attack a president and the Geneva Conventions are clear. Can our UK ambassador attack the prime minister?"
One of Africa's longest-serving leaders, Museveni has come under increasing criticism over an alleged failure to tackle widespread corruption and a reluctance to cede power.
Graft is deeply entrenched in Uganda and Museveni's government has previously shown little appetite to crack down hard. Many Ugandans believe he is preparing his son, Kainerugaba Muhoozi, to take over when he retires.
A private letter by General David Sejusa, the head of internal security and long regarded as close to Museveni, called for an investigation into allegations of a plot "to assassinate people opposed to Museveni's succession plan".
In May, Uganda shut down for 10 days the Daily Monitor and one other paper and two radio stations for carrying reports about Museveni's succession and saying that there were plans to assassinate those opposed.
The government allowed them to reopen only after they said they had accepted a range of restrictions.
Kainerugaba, who has been rushed through the ranks to his present rank of brigadier general, commands the army's elite presidential guard that also provides security for Ugandan oil fields near the border with Democratic Republic of Congo.