The AFL stuck by its controversial rejection of the new World Anti-Doping Agency (WADA) code, despite growing misgivings among club officials.

While cricket and rugby league agreed to sign the new accord by Thursday's deadline, the AFL stuck to its stance and put at risk about $1 million in federal government funding.

The AFL is isolating itself in Australia and will also be one of few sporting groups worldwide not to agree to the code.

Collingwood coach Mick Malthouse became the latest club official to question the AFL's position, but league chief executive Andrew Demetriou was resolute.

Demetriou said the league would put its case to WADA directly and was open to further talks with Federal Sports Minister Rod Kemp.

The AFL boss added one of the key reasons for the refusal was its collective bargaining agreement with the AFL Players Association (AFLPA).

That agreement is not due to be reviewed until next March.

But the league would have to change provisions of its anti-doping code to comply with the WADA accord, meaning changes to the collective bargaining agreement.

Significantly, the AFLPA publicly supported the AFL and called on the government not to withhold funds because of the league's WADA stance.

Demetriou stressed the importance of having the players on-side.

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