Requests to accept the landing of RNLI boats carrying 120 migrants intercepted off the Isle of Wight were refused by both Portsmouth harbour and Southampton Port.
When the migrants were landed on Sunday at Eastney, in Langstone Harbour, anti-migrant protesters blocked the road.
Associated British Ports (ABP), which operates Southampton, said it was not the closest port and it “did not have suitable reception facilities available”.
The understands the King’s Harbour Master (KHM) Portsmouth also declined a coastguard request, but it would not comment directly on operational matters.
The protest followed a separate demonstration at the Port of Dover on the previous day.
The Langstone Harbour Master said the migrants were “recovered” onto two RNLI vessels in the vicinity of the Nab Tower.
They said they would have travelled at “quite a slow speed” to Langstone because the vessels were so overloaded.
An RNLI spokesperson said: “We are working with the relevant parties to understand the decision to deny access, and we are disappointed with the nature of the communication with our crews, who voluntarily give their time to save the lives of others at sea.”