Unfortunately our government filters the SSH protocol so now we can't connect to our Linux server.

They do the filtering by checking the header of each packet in the network layer (and not by just closing port). They also do away with VPN protocols.

Is there any alternative way to securely connect to a Linux server?   

From what I heard earlier today, https/ssl flows correctly through your borders.

You should hence check out Corkscrew.

Similarly to netcat, it's used to wrap ssh in https to allow the use of https proxies.

Another solution would be to use LSH which, by having a different signature than ssh, works from Iran as Siavash noted it in his message. 
