Some students had planned to apply for their loans online after the company's website advised them the service would be available in April, well before the deadline of 2 July for new applicants and 28 May for those who already have loans.
Now students are being advised to use paper-based systems, although the company assured them their loan payments would not be delayed.
"We had planned to launch the new website in April but, for business rather than technical reasons, we have now decided to release the portal in stages," a spokeswoman said.
"A phased launch is considered prudent to accommodate the difficulties of introducing substantial operational and IT changes in the company and in the local education authorities.
"It was considered unwise to introduce further administrative complexity in one step. Our approach throughout this project has been one of caution and rigorous adherence to best practice."
About 3% of this year's eligible applicants have registered their interest in applying online and 97% have elected to apply on paper. There is no need for the company to print more paper forms as a result of the delayed launch of the web-based loan applications.
Some students have complained that the company kept them in the dark about the delay to the new system, but the Student Loan Company insisted it had kept applicants well-informed of the process.
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