Uganda’s army spokesman Lt Col Paddy Ankunda said that the “threat of terrorism is real”.
The head of Kenya’s police, Joseph Boinnet, echoed those comments on Twitter and called for the public to be alert.
Both Uganda and Kenya have experienced attacks by the Somalia-based militant Islamist group al-Shabab.
In April this year 147 people died when a university campus in the Kenyan town of Garissa was attacked.
That followed the September 2013 attack on the Westgate shopping mall in Kenya’s capital, Nairobi, in which 67 people were killed.
In July 2010, more than 70 people died in Uganda’s capital, Kampala, when a bar and restaurant were bombed as people were watching the World Cup final.
In Nairobi on Sunday there were more police officers outside churches and shopping malls, reports Kenya’s Standard newspaper.
Correspondents say increased concern amongst members of the public is evident.
Uganda’s police spokesman Fred Enanga told journalists on Sunday that police have “heightened [the] level of alertness” and that they are working with the military “to ensure that all Ugandans and visitors are safe”.
Kenyan and Ugandan soldiers are part of an African Union force in Somalia which is helping the government battle al-Shabab.
Kenya’s Defence Minster Raychelle Omamo expressed solidarity with the people of France.
“What is important is that we continue to work hard to eliminate this threat, to continue to work as a collective to further the cause of peace, stability of good will and of freedom in our countries,” she told the BBC’s Focus on Africa radio programme.
Five Africans are now believed to have been among the 129 people killed in the Paris attacks.
Moroccan architect and teacher, Amine Ibnolmobarak, aged 29, has been named by the Moroccan Times newspaper as one of those killed at the Carillon bar.
Two Tunisian women, sisters from near Bizerte aged 34 and 35, were also killed, according to France’s BFM TV. They were celebrating a friend’s birthday.
And two Algerians were killed, the official APS news agency said, citing diplomatic sources as saying the victims were a woman aged 40 and a man aged 29.
Two Senegalese nationals also died in the attacks, according to Senegal’s media.