"This agreement... is frightening," a spokesman for the association of Rwandan refugees in Mozambique told AFP.
"We would like it to be used for justice, but recent events lead us to believe that it is persecution," he said, asking not to be named.
A number of Rwandan dissidents have been murdered or forcibly disappeared in southern Africa in recent years.
A former Rwandan lieutenant was shot dead in a Maputo suburb in 2021, and in 2012 the body of the former head of Rwanda's Development Bank was found floating at sea off the capital.
Mozambican government spokesman Filimao Suazi said that extradition treaty covers past and future crimes and sentences.
Several thousand Rwandan refugees live in Mozambique, according to United Nations figures.
Most settled in the country after the 1994 Rwandan genocide that cost the lives of some 800,000 people.
Rwanda's President Paul Kagame has ruled with an iron fist ever since.
The treaty targets genocide fugitives "and other suspects or convicts".
According to Rwanda's Genocide Fugitives Tracking Unit, 13 genocide suspects live in Mozambique.
But opposition leader Victoire Ingabire, a fierce critic of Kagame, told AFP the treaty was open to abuse.
"People flee countries for political reasons and persecution and the government can use such treaties to persecute people and to make up crimes just to get them extradited," she said.
The text initially signed in Kigali in June was formally approved by the Mozambican government Tuesday, paving the way for ratification by parliament.
The Rwandan senate ratified the treaty earlier this week.
Rwanda is regularly accused of chasing after opponents in exile, a charge Kigali has always denied.
At a signing ceremony in June, Rwanda's legal affairs minister Soline Nyirahabimana said the treaty meant the two countries were "now safe from criminals".
Kigali has helped Mozambique fight an Islamist insurgency in the gas-rich north of the country, deploying more than 2,000 troops and returning large swathes of the region under government control.