"It may not have come across as intended," he said.
Mrs Beamsley should have been allowed in the store in her motorised wheelchair, he said.
The "no mobility scooters" policy was put in place after a volunteer was seriously injured after an accident in the store this month, Mr O'Fee said.
The volunteer was put in hospital after a person lost control of their mobility scooter, crashing into shop stands.
"It wasn't just a small accident, it was quite serious," Mr O'Fee said.
"For public safety, we need to keep them outside.
"We're not banning the individual, we're just saying we prefer you to keep your scooter outside.
"It's just the scooters - no one's banned."
Signs have been put up in the shop window advising customers of the mobility scooter ban.
Mr O'Fee said shop volunteers were happy to assist people by getting items for them, and the policy was about eliminating risk and "covering ourselves in the event of someone taking us to court".
The ban applied to the Whanganui, Feilding and Palmerston North stores but was not national policy, he said.
"Obviously, we've had an incident in the shop where someone was injured and we've made a policy.
"I wouldn't want our policy to be seen in a bad light," Mr O'Fee said.
Meanwhile, Mrs Beamsley said she had accepted the apology from the SPCA. "The manager was very apologetic and I have accepted the apology."
Whanganui Disability Resources Centre manager Les Gilsenan said he had no problem with shops not allowing mobility scooters in-store - the centre itself had banned mobility scooters inside.
But he said electric wheelchairs should be allowed, especially where people had no mobility.
