Experts from the World Health Organisation (WHO) arrived Friday in the affected village in North Sumatra to help investigate a possible outbreak after three people died and the 13 were admitted to hospital.
"All specimens collected from suspect cases have given negative results. They are all recovered," I Nyoman Kandun, director general of the ministry's communicable diseases department said on a text message.
Officials and residents in Asahan district in North Sumatra province said villagers began showing symptoms of avian flu after a large number of chickens died suddenly last week in Air Batu village.
The local husbandry office took preventive action this week by slaughtering and burning some 400 chickens and ducks.
The ministry, which has stopped giving regular bird flu updates, announced earlier this week that the human toll from avian influenza in Indonesia had risen to 112 following the recent death of a 19-year-old man.
The deadly H5N1 strain of bird flu has killed more than 240 people worldwide since late 2003.
The virus typically spreads from bird to human through direct contact, but experts fear it could mutate into a form easily transmissible between humans, with the potential to kill millions in a pandemic.