Allegations that Robert Kyagulanyi and Francis Zaake were tortured have triggered widespread protests in the capital Kampala and other parts of the country.
Museveni, who has been in power for 32 years, frequently replaces ministers and other top government officials without publicly giving explanations.
Kizza Besigye was arrested 3 times this week and said police have put him under house arrest.
In March Sweden suspended some assistance over Uganda's anti-gay laws.
Police say the boat was overloaded, a common factor in similar tragedies in the east African country.
Activists say the new legislation infringes on fundamental rights to privacy and non-discrimination.
EWN's Africa Correspondent, Jean-Jacques Cornish, reports on the day's top African news
