Shaun Harvey defended the decision to ensure Pompey and Southampton were not drawn together in this season’s Checkatrade Trophy.
The Football League chief insisted both clubs had requested to be split up in the pot.
The south-coast rivals haven’t met since the 2-2 Championship draw at St Mary’s in April 2012.
The Checkatrade Trophy is mainly made up of League One and Two teams but also includes 16 invited under-21 sides from clubs with category one academies.
Pompey have been drawn alongside Fulham under-21s along with Charlton and Crawley.
However before the draw started for the eight southern groups, Southampton’s ball was removed from the pot and a separate draw was made for group A, which already featured Charlton, Crawley and the Blues.
After that, the draw preceded as normal, with Southampton eventually going into group H with Cambridge, Northampton and Peterborough.
Harvey said: ‘One of the commitments we made right at the outset was to try to avoid group-stage games that had a significant potential for high levels of disorder.
‘Previous experience with Portsmouth-Southampton games, particularly when talking to Portsmouth, was that there does appear to be potential for that when they’re drawn together.
‘So if we could avoid that in the group stages then it was a conscious decision that we should do so.’
However, Harvey admitted a Pompey-Southampton clash will go ahead if they meet each other later in the competition.
He added: ‘We want a profile for the competition but it’s about balancing risk.
‘We could have crossed our fingers and we would have had a one-in-eight chance but we did say we would look at the structure of the groups to avoid that particular issue.
‘They could meet each other later in the competition, in which case it’s a straight knockout draw and the game will go ahead.
‘But why create the potential for negative publicity around the game if you don’t need to?’