The Indonesian football association says it is awaiting the results of a full investigation and will appeal if it finds the suspension "not fair".
Aji Santoso received the suspension after he was sent to the stands during a 10-0 loss to Bahrain in February for claiming money was influencing the outcome of the match refereed by Lebanese referee Andre Al Haddad.
The coach of the Indonesian under-23 team was acting as caretaker coach of the senior side when in the 75th minute of the Bahrain match he was overheard by an official saying: "There is money (involved) here."
Bahrain needed to beat Indonesia by a nine-goal margin to have any hope of reaching the next round of qualifiers.
Following the match FIFA launched its own investigation into the result as well as suspending and imposing a fine on Santoso for his behaviour.
On Thursday Bob Hippy, of the Football Association of Indonesia (PSSI), said: "FIFA's sanctions are one-sided. We'll wait for them to announce the results of the full investigation and will appeal if we find the suspension is not fair.
Santoso told AFP he fully accepted the suspension "in good spirit".
"I respect FIFA's decision. I take it as a lesson to better manage my emotions on the field," he said, adding that PSSI would pay the Rp 60 million ($A6100) fine.
PSSI has been in hot water with FIFA and the Asian Football Federation in recent years over poor management, corruption allegations and leadership tussles.
FIFA has given PSSI a June 15 deadline to reconcile two competing top-tier football leagues that have split the nation's best clubs and seen star players kicked out of the national team.