Have you set the float valve to allow filling up to the mark as if there isn't enough water in the cistern you WILL have to pump it. If it fills to the correct level and you still lhave to pump it, then yes it's a fault in the diaphragm and it needs changing. The quickest is to change the whole flush unit for one that doesn't have to be removed to change the diaphragm.
If the toilet is new then call the shop where you got it and tell them the problem then ask them if they will pay for a plumber to put it right [Sale of goods act] it's not of merchantable quality in short it don't work.
bob
February 2005