Toni has played just once for the first team this season - in a German Cup game - and twice for the reserve side, who play in the third tier of the German league.
The Italian forward has hinted he would no longer be willing to play in the reserves and his remarks add to van Gaal's problems this weekend.
Winger Arjen Robben limped off before half-time in Wednesday's goalless draw at home to Juventus in the Champions League while there have also been rumblings of discontent from forward Mario Gomez, who was dropped for the last two matches.
Toni insisted he had recovered from an Achilles tendon injury and was widely quoted in German media as saying he would not play another reserve game.
"He (van Gaal) wants me to keep playing in the third division," said Italian Toni. "I don't think I will be doing that again.
"I feel fit and it's a shame I wasn't picked against Juventus. I would love to have played against my friends from the national team."
Bayern sit seventh in the Bundesliga and have failed to score in their last two games - a 1-0 defeat by Hamburg SV last Saturday and Wednesday's match with Juventus.
Gomez, who became the Bundesliga's most expensive signing when he moved form VfB Stuttgart in May, will have to seize his chance if he is picked.
Before being dropped he had complained about being substituted too often but was given a public reprimand by general director Karl-Heinz Rummenigge, who told him to work harder.
Cologne will be without suspended Portugal midfielder Maniche, who was banned for three games after being sent off against Bayer Leverkusen.
Hamburg SV, who lead on goal difference from Leverkusen, visit bottom club Hertha Berlin on Sunday. Hertha fired Swiss Lucien Favre after losing six league games in a row and shipping nine goals in their last two.
Under-23 coach Karsten Heine has taken over on an interim basis. Leverkusen host Nuremburg on Saturday.
NEWS: Narked Toni edges nearer January exit
NEWS: Toni issues Bayern ultimatum
