Presidents Ellen Johnson Sirleaf of Liberia and Ernest Bai Koroma of Sierra Leone were in Conakry for the closed-door talks with their Guinean counterpart Alpha Conde, joined by Ivory Coast Foreign Minister Charles Diby Koffi.
The Guinea health ministry said Saturday that 81 people had died of Ebola from 127 confirmed cases of the disease. Liberia has reported 13 cases of haemorrhagic fever of which six were confirmed to be Ebola, with 11 deaths overall.
Suspected cases have been reported in Sierra Leone and Mali, sparking fears that it could spread throughout the region.
But Conde said during a visit to Geneva, home of the World Health Organization (WHO), on Wednesday that Guinea's Ebola outbreak is under control.
In a sign of subsiding concerns, Senegal, which had closed its border with Guinea, reopened the frontier on Tuesday, Conde said.
On Sunday, the summit's final communique "hailed the efforts of each member state and, in particularly Guinea, to contain the spread of the Ebola epidemic and to stress the need to continue medical monitoring at the borders, in order to eradicate this scourge in the sub-region."
Working with the WHO and aid groups, Guinea remains on high alert against the virus, an incurable disease that can kill up to 90 percent of its victims.
There is no vaccine or cure for Ebola, which can be caught from handling the blood or the bodily fluids of sick or dead forest animals.
The Mano River Union, named for the waterway that begins in the Guinea highlands and forms a border between Liberia and Sierra Leone, was set up in 1973.
Other agenda items for Sunday's meeting include economic cooperation, regional integration and cross-border security, officials said.