Derry director O'Doherty said that measures had been planned to ensure the safety of Rovers fans at Friday's game.
"The attacks occurred outside the ground and they were carried out by children," Mr O'Doherty told RTE.
"I don't want to minimise this in any way because first of all I want to apologise to any Rovers fan and indeed the owners of the buses but it did happen outside the ground.
"No League of Ireland club has jurisdiction for outside its ground.
"However, we recognise the special situation of The Brandywell.
"In recent games, such as the Bohemians game, our stewards stayed on and made sure there was clear and safe exit and that was offered.
"Unfortunately I think the Rovers guys had already made up their minds on this. It is regrettable and I'm extremely sorry they have taken this stance."
O'Doherty added:"If Shamrock Rovers decide they need a police escort to come to the ground that is entirely up to Shamrock Rovers.
"One situation has been taken here and used to make something that is not true overall.
"The vast, vast majority of visiting fans come to the Brandywell and never have the slightest problem."
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