On Tuesday night, SmartyHost migrated several thousand sites from Primus to its new hosting provider, Optus.
SmartyHost managing director Anoosh Manzoori said his company had e-mailed customers the Sunday prior to the migration, asking them to change their username to a five-digit number, a security requirement of the new facilities.
However, some long-standing customers had not kept their contact details up to date, and did not receive the message, Manzoori said.
This meant their sites were not available once the changeover occurred, he said.
"This is not an outage situation, it's an upgrade to a better service.
"The main problem is on a site-per-site basis where the DNS hasn't propagated.
"So we have to verify who they are, and change their e-mail address or other details."
The new system allows customers to update their contact details in real-time.
Several SmartyHost customers have complained about the migration to ZDNet Australia.
Complicating matters, global domain name registry VeriSign suffered an outage with its domain name system services around the time of the migration, according to Manzoori.
This meant anyone making such a change had to wait another 24 hours before the redirected IP addresses would be recognised and take effect.
"The technical problems weren't all under our control," he said.
SmartyHost also encountered problems with its phone systems last week, and had asked technicians to restore normal service.
"We've hired additional staff and have contracted a call centre to call every customer affected and help them," he said.
It would take "another day or so" to call all affected customers, Manzoori said, by which time he expected the issues to be resolved.
There would also be a compensation offer for those affected, he said.
"We'll be sending a formal letter with compensation on the monthly account [fee]."
While unsure of the number of customers affected, Manzoori said it was a "minority".
"We're not sure on the numbers, there's so much duplication in the support system.
"But we're giving priority to the phone [requests]," he said.
SmartyHost launched an online chat facility on Friday to help affected customers contact the company.
Manzoori said another reason for some customers not being migrated was non-payment of outstanding bills.
The customer migration problems come after SmartyHost made a bid for the high-end corporate market last week with the launch of its new SmartyCorp service.
SmartyHost has 25,000 customers and claims to be the number two Web hosting provider in Australia behind WebCentral.