Rob Whiteman said UKBA computer systems are “prone to falling over”, and that the issue was “a constant frustration”.
His comments come as an immigration lawyer warned the delays could be costly to the UK economy.
The system collapsed after a recent surge in visa and permit applications.
UKBA chief executive Mr Whiteman said the problem was caused by a network error that could happen again and could affect several applications.
Hundreds of foreign nationals were turned away from the Croydon Enquiry Office in London on 3 May when the computer system froze.
Many were from outside the EU and were waiting to be seen for biometric visas or residence permits.
Mr Whiteman told MPs on the Commons home affairs select committee: “In terms of UKBA improving over the next couple of years, some of the things are quick.
“[Information technology] is going to be a recurring theme, and what we have to do at the moment is put in place some reviews and studies.
“The systems are still prone to resilience problems and that will not be put right overnight,” he added.
Meanwhile Andrew Tingley, a partner at law firm Kingsley Napley, warned the delays could lead senior executives and foreign investors to consider taking their business outside of the UK.
The immigration lawyer said it was “beyond farcical” that the identity rules for non-EU residents had left the UKBA’s systems unable to cope.
In April, the UKBA was heavily criticised for allowing long queues to build at Heathrow airport’s passport control, with some passengers claiming they waited over three hours to enter the country.
It has since emerged that the agency failed to meet its April target at Heathrow for processing most passengers from outside the European Economic Area within 45 minutes.