Some employers were worried about being fined if they did not register before a deadline next week.
One business owner told the BBC he had been unable to get onto the website since Monday.
However, the regulator said the website was now up and running again.
A spokesperson said that customers should be able to get onto the website without difficulty, but anyone facing problems should call the helpline, on 0345 600 1011.
Thousands of small businesses with between one and 19 employees are currently having to tell the regulator how they are conforming to the new pension rules.
Under the law, anyone over the age of 22 and earning more than Â£10,000 a year has to be offered a pension.
A computer glitch at The Pensions Regulator - which prevented employers from registering for auto enrolment pensions - has now been fixed, the regulator has said.