The encapsulation dot1Q 1 native command was added in Cisco IOS version 12.1(3)T. If you are using an earlier version of Cisco IOS, then you need to use 802.1Q configuration for Cisco IOS Versions Earlier than 12.1(3)T
Here is an example of how to do that:
c2600#configure terminal
Enter configuration commands, one per line. End with CNTL/Z.
!-- Select FastEthernet 0/0 for the trunk configuration.
c2600(config)#int fastEthernet 0/0
c2600(config-if)#no shut
!-- Note that the IP address for VLAN1 is configured on the main interface,
!-- and no encapsulation for VLAN1 will be done under the sub-interface.
c2600(config-if)#ip address 10.10.10.1 255.255.255.0
c2600(config-if)#exit
!-- Configure dot1q encapsulation for VLAN 2
!-- on sub-interface fastEthernet 0/0.2.
c2600(config)#int fastEthernet 0/0.2
c2600(config-subif)#encapsulation dot1Q 2
c2600(config-subif)#
!-- Configuring L3 information on the sub-interface 0/0.2.
c2600(config-subif)#ip address 10.10.11.1 255.255.255.0
c2600(config-subif)#exit
c2600(config)#^Z