The move came because the markers had still not been allocated supervisors to carry out initial checks on their work by last weekend, more than three weeks after the tests were taken, Edexcel admitted.
Examiners were supposed to be sending back a final batch of scripts to their supervisors for final checks by yesterday, and to complete all their marking by Monday, June 13. The affected examiners now have until June 30 to mark their scripts.
Edexcel and the Qualifications and Curriculum Authority said more than 11,000 markers had been recruited for all key tests this year and that in most cases the marking was going smoothly.
The deadline extension follows reports of chaos surrounding the marking arrangments. One marker with 20 years' experience said the administrative problems were the most serious he had known.
He had repeatedly tried to call and email Edexcel because he had still not been assigned a supervisor, but received no answer.
He said: "I've never seen anything in my life as incompetent as this. I'm absolutely appalled."
The TES online staffroom includes similar complaints.
The claims come with Edexcel, which this year begins an pound;80 million contract to mark the tests, and the QCA under intense pressure. Last year, a marking fiasco led to the resignation of the head of the National Assessment Agency.
A QCA spokesman said the extension affected only a small number of examiners and would not delay the release of KS3 results to schools in August.