The fourth phase of ticket sales for the FA Cup semi-final began at 6am with 6,500 tickets selling out in just over two hours.
But some fans had difficulties in getting tickets as the reference number they needed to buy online from Ticketmaster was not accepted.
The fourth stage was open to non-season ticket holders on Pompey's database, which required them to get the client reference number from the club.
Sandra Leat, from Farlington, tried to get tickets for her husband and her nine-year-old son, but was told her reference number was not valid.
She said: 'We called the club three times yesterday to get the client reference number but online it's not recognised on the database.
'It's such a shame because we thought going on the internet would make it much easier.
'Getting up at 6am to make phone calls is bad enough but going on the internet would have been perfect.
'It's frustrating. You can't get hold of anyone at that time of the morning.'
But Rick Strang, from Tunbridge Wells who was born in Portsmouth, managed to get tickets over the phone.
But he says he was informed by the operator that the client reference number wasn't necessary and that it would be checked by the individual credit card.
'They are not interested in the client reference number at all. I could be anybody,' he said.
'If we get to Europe next year and there are big European games what are we going to do then? It's going to be a shambles.'
Some season ticket holders have questioned why the online service was not available from the start.
Gary Double, director of communications at the club, said: 'The tickets didn't go on sale online in the earlier phases due to technical difficulties, which have now been overcome.'
Mr Double said that the club was also trying to contact Ticketmaster about the issues raised by fans this morning.

How to get to the match
After four separate phases of ticket sales, there is now only one authorised way of getting a ticket to the FA Cup semi-final between Pompey and West Brom.

• A batch of 1,180 tickets will go on sale from the club's ticket office at 9am on Wednesday, April 2.


• They will be available to season ticket holders only and be limited to two per person.


• The seats are those left over from the first phase of ticket sales plus 80 Club Wembley seats.


• The tickets will be sold on a first-come, first-served basis.