after beating the three team rocket guys in that gastly tower you can talk to Mr Fuji, he will give you the pokeflute
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You can find the Poke Flute in the Pokemon Tower. After you free Mr. Fuji, he will give you the Poke Flute.
In poke platinum you get a black poke flute from Looker the agent
Heres a big cheat to get the poke flute go to celadon city and buy a poke doll located on floor 4 then go to Pokemon tower then find the ghost that block's the stairs then use the poke doll to flee and go upstairs and beat the rockets then get the poke flute.
To get the poke flute on silver you need to go to the radio tower in lavender city, talk to the man inside and he will upgrade the radio on the poke gear. You should then be able to find the poke flute radio broadcast.
There is no Poke Flute item in Pokemon Silver. Instead, the player can have their radio upgraded in Lavender Town. It will then play a station that can play the Poke Flute tune.