HM Revenue and Customs (HMRC) said users of its online service were still experiencing delays filing their tax self-assessment.
The system is recovering from the breakdown on Thursday when the website was out of action for several hours.
HMRC was forced to extend the self-assessment deadline until midnight on Friday.
HMRC says Friday's delays are not as serious and most users should be able to access the site without delays.
Appeals process
"We're very busy at the moment and some people are being delayed". said HMRC spokesperson, Claudine Lashley.
"This is getting ridiculous. I'm trying to submit my tax return under the threat of a fine or appeal at best and the HMRC site is again failing to work."
Anyone that fails to file by midnight tonight faces an automatic £100 fine plus interest on any tax due if they missed the original midnight deadline.
But there is an appeals process and HMRC says anyone who feels they have been fined unfairly will be dealt with on a case by case basis.
HMRC estimates that around 34,000 will complete their self-assessments on Friday, that compares with 204,000 returns that were submitted on Thursday.
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