Are you using ISL style vlans?
If so - here is one possible solution to configure on your router :-
interface FastEthernet1/0
description VLAN Trunk
no ip address
no ip directed-broadcast
full-duplex
!
interface FastEthernet1/0.1
description Peernews
encapsulation isl 99
ip address a.b.c.d 255.255.255.252
no ip redirects
no ip directed-broadcast
!
interface FastEthernet1/0.2
encapsulation isl 100
ip address a.b.c.d 255.255.254.0
no ip redirects
no ip directed-broadcast
no cdp enable
!
interface FastEthernet1/0.3
encapsulation isl 101
ip address a.b.c.d 255.255.255.252
no ip redirects
no ip directed-broadcast
no cdp enable
In this example, from which I've removed our addresses, you set up the physical layer information on the physical interface, and use pseudo interfaces for each vlan. The encapsulation command specifies which vlan the pseudo interface is for.
Hope this helps.
Regards
Neil