In my application the transformer input required is 220 volts. As the potential difference between phase and neutral available is less than 220 volts, can I connect two phases lines with a potential difference of 220 volts as input to the transformer? If yes, what difference can it make in the circuit?

 

Yes, it's OK to connect between two phases provided you protect both primaries with a fuse or 2 pole breaker, that's done all the time for control transformers.

The only difference is the phase angle. If you need the secondary to be in phase with something, e.g. for firing an SCR it could be a problem.

Roy