Malawi's Minister of Homeland Security Ken Zikhale Ng'oma said Kigali lodged an official request for assistance as it seeks to locate the suspected "warlords".
"The Rwandan government has sought assistance from the Malawi government in identifying 55 suspects who are currently hiding in Malawi. These individuals are known warlords," Ng'oma told a press conference in the capital Lilongwe.
Around 800,000 Rwandans, most of them ethnic Tutsis, were slaughtered over just 100 days in 1994 at the hands of Hutu extremists.
The suspects allegedly hiding in Malawi are wanted in connection with "the deaths of over 2,000 people in some churches," Ng'oma said, giving no further details.
Rwanda's request comes weeks after Fulgence Kayishema, one of four remaining fugitives sought by UN investigators for their role in the genocide, was arrested in South Africa after more than two decades on the run.
Kayishema, who used many aliases and false documents, is thought to have travelled on a Malawian passport.
Ng'oma said authorities were "conducting thorough investigations" into how the now 62-year-old acquired the document and would be providing "a comprehensive report soon".