Trouble for Capt. Mike Mukula started with the fund from the Global Alliance for Vaccines and Immunisation (GAVI), which dates back to early 2004.
Uganda had surpassed national immunization targets for 2002 and GAVI rewarded it with more funds to continue the work.
In January 2004, the executive director of GAVI, Dr. Tore Godal, formally informed the then health minister Jim Muhwezi, of the $4.3m (about sh7.6b) reward.
The money was remitted in two disbursements. Later queries were raised that sh1.6b of that money was not accounted for.
According to the Inspector General of Government (IGG ) who started proceedings against the three health ministers, the money was mismanaged in 2005 under their watch.
The trial was started but stalled. However, it resumed in 2012 and on June 17, 2012, two ministers, Jim Muhwezi and Alex Kamugisha were cleared by court, which ruled that there was no evidence against them.
For the third minister, Mike Mukula, however, court ruled that he had a case to answer and, therefore, should defend himself regarding the misappropriation of sh210m that he received.
In his defence, Mukula said he signed for sh263m for health advocacy, but denied any fraud saying he never received the money.
"I did not see the money. I did not receive the money. I did not even smell the money,"Mukula said.
He said the permanent secretary Jethro Mugumya instructed that the money he requisitioned be given to Jim Muhwezi, but also clarified that Muhwezi never received the money either.
"As a minister I was aware that sh54m was paid to the office of the First Lady and sh210m was re-banked in Bank of Uganda," Mukula said.
He added that he later learnt that sh54m was refunded by Margaret Lalam, from First Lady's office, and it was well accounted for.
He explained to court that the money was deposited in Bank of Uganda in five installments on directives of the permanent secretary.
However, the investigating officer, Amos Victor Acidri produced a payment voucher indicating that Mukula received the money.
A former account assistant in the health ministry, Lydia Nalwanga, told the Police in 2006 and later testified in court that Mukula refunded the money.
She said that Mukula signed for the money because someone needed to take responsibility for the money being signed for.
He refunded it after nine months and only after IGG had instituted inquiries into the mismanagement of the funds. Nalwanga said when Mukula was signing for the money he indicated the reason as "facilitating the movement of the money" but such a provision never existed on the voucher.
In its judgment on Friday, court said Mukula embezzled sh210m, claiming it was used for a conference in Mt. Elgon Hotel in Mbale.
The Magistrate, Irene Akankwasa, noted that Mukula signed for the money and, therefore, had to take full responsibility.
She further noted that Mukula used his official position to sign for sh263m purportedly for the First Lady's office and fraudulently retained sh210m and only availed sh54m to the First Lady's office, which was accounted for.
The Magistrate noted that Mukula requisitioned for the money on February 11, 2005 and received it on February 17, 2005.
He only started refunding the money on October31, 2005 in bits until May 31, 2006.
The Magistrate ruled that the fact that Mukula refunded the money in bits and at his own will, meant that he had the intention to steal and deprive the beneficiary from utilizing the money.