Ugandan government spokesman Robert Kabushenga has been appointed chief executive officer of the state-owned newspaper, New Vision.
Mr Pike had held his position at the paper for 20 years
His appointment follows the departure of former managing director William Pike, who held the post for 20 years.
The shake-up comes a week after the paper ran a story saying the Ugandan army was resuming the war against the Lord's Resistance Army rebels.
Correspondents say the appointment raises questions about press freedom.
The government feared last week's New Vision story would jeopardise peace talks with the LRA in the south Sudanese town of Juba.
The main independent newspaper in Uganda, The Monitor, reported that Mr Pike had been sacked.
But a statement issued by the New Vision's board of directors said Mr Pike had resigned but agreed to stay on for a three-month handover period.
Earlier this week, President Museveni criticised the New Vision in his independence day speech.
The government has an controlling stake in the daily newspaper of about 80%.
But the BBC's Sarah Grainger says many people thought the Mr Pike prevented it from being purely a government mouthpiece.
"There was a feeling from high up that William Pike was too independent and did not throw all his weight behind the government's project to amend the constitution," Peter Mwesige, head of mass communications at Mkerere University told the BBC's Focus on Africa programme.
However, Mr Kabushenga told the same programme that the change was not the result of President Museveni wanting to appoint sycophants.
"I think the president himself is very interested in a very powerful editorial product that is credible and that can assist Ugandans," Mr Kabushenga said.