The commandant of the Special Investigations Division (SID), Charles Kataratambi, has been arrested.
He is accused of mismanaging a case.
He was detained at Nsambya Police barracks cells.
Kataratambi was on Wednesday suspended from office pending investigations into alleged professional misconduct by him and some of his officers.
He was however arrested yesterday morning reportedly on instructions from President Yoweri Musevni to Police Chief Kale Kayihura.
Kataratambi was arrested together with two other officers whose identity is yet to be revealed but are believed to be his right hand men.
Fred Enanga, the police spokesperson could neither deny nor confirm the arrest when contacted by Uganda Radio Network but says he was aware that the Commissioner is being investigated by the Professional Standard Unit.
He declined to divulge information on the investigation.
According to sources, the police boss was arrested after a complaint was presented to the president against his conduct while investigating a case of fraud in which, a number of people are alleged to have connived and stolen $1.45 million (4.2billion Shillings) from Equity Bank.
The case in which Equity Bank is the complainant was filed at Jinja Road Police in March 2015, and later the file was forwarded to SID.
The police file indicates that three people withdrew money to a tune of $1.45million (4.2billion Shillings) from Equity Banks Oasis mall branch from an account owned by a South Sudanese national.
10 minutes after the withdrawal, the account owner also withdrew the same amount at a branch in Juba, South Sudan capital.
The bank only realised the double withdrawal three days day later.
Three suspects, whose identity have been withheld not to compromise investigations, were in the first week of investigations arrested and after about a month in detention, one of the suspect revealed that he had part of the money.
The suspect says in a written statement he made to the investigating police officers that $450,000 was in his house and said his wife would hand it over to the police.
However, police record indicate that the suspects were later released on police bond but there is no record of whether the money was recovered from the suspect’s home.
On Friday last week, James Mwangi the Equity Bank CEO met with President Museveni at State House Entebbe and reportedly complained about the disappearance of the recovered money.
In their complaint to the president, Equity Bank top management claimed that the police officers investigating the crime acted unprofessionally during investigations prompting the president to order their arrest.
Katarambi has handled several prominent cases including the Mukono-Katosi road fraud and the murder of Police ASP Joseph Bigirwa.