The 22-year-old Peralta joined up with his teammates at a training camp in the Austrian town of Villach on Sunday. The rest of the team arrived Saturday.
The country's football federation didn't provide any other details about Peralta's visa issue.
Honduras is in Group D and its first match is against Morocco on July 26 at Hampden Park in Glasgow, Scotland. Spain and Japan are the other two teams in the group.
Honduras will play three warm-up matches for the London Olympics against Gabon, United Arab Emirates and Egypt.