Wada wanted the suspension to be increased to two years, but Guerrero also appealed in the hope it would be annulled.
The FPF said in a statement that it "profoundly regrets the lengthening of the ban imposed on our player Paolo Guerrero who has always shown exemplary conduct".
The worldwide governing body of soccer Federation Internationale de Football Association lowered the embargo by half, six months, but the World Anti-Doping Agency filed a petition before the Switzerland-based Court of Arbitration for Sport to increase the punishment to between one and a couple of years.
Guerrero tested positive for Benzoylecgonine - which is a metabolite of cocaine - at a 2018 World Cup qualifying game against Argentina in October.
Announcing the extension of the ban now ending in January 2019, CAS said it was the most appropriate course of action considering Guerrero's degree of fault in the matter.
"Both FIFA and the Court of Arbitration for Sport agreed Guerrero did not knowingly ingest the substance and that there was no performance-enhancing effect".
However, CAS partially accepted an appeal from the World Anti-Doping Agency (WADA) which had requested the sanction be increased to between one and two years.
Guerrero's appeal against the ban was upheld. A fan said that he had been looking forward to the World Cup, but with Guerrero's ban, there was nothing to be excited about anymore.
The player and his representatives have claimed he was not taking any drug and was accidentally consumed through tea, according to AS.
It is the second ruling from sport's highest court that has weighed heavily on Peru's first World Cup appearance in 36 years.
He has scored 32 goals in 83 appearances and is a galvanising presence for his team.
CAS said that Guerrero bore "some fault or negligence, even if it was not significant, and that he could have taken some measures to prevent him from committing an anti-doping violation".