The School Curriculum and Assessment Authority has confirmed that the Northern Examinations and Assessment Board is also looking at other scripts graded by the same external marker.
SCAA sees the Wirral case as different from the other complaints about the marking of the English tests.
A spokesperson said: "We regard this as a completely anomalous one-off incident, but we take it very seriously, and are confident that the board will take whatever action is appropriate."
However, the head of the school concerned, Peter Johnson, of Wallasey comprehensive, said: "It just reveals to me that the checking procedures are totally inadequate."
The school governors have written to SCAA to voice their concern. They say that after the late arrival of the marked scripts, "while checking the scripts in school, it became evident that some were missing, some showed evidence of not having been fully marked and comparisons between scripts showed inconsistencies in the marking."
When the missing scripts turned up, "it then became evident that the scripts had not been marked.
"They apparently had no mark allocation on the front cover, nor did they have any mark on the answers inside."
When the school checked the mark sheet, they found that for each of the 12 candidates concerned, a mark had been entered into the mark sheet, the marks for both papers had been totalled and a level had been awarded.
Later, staff discovered that six papers are still missing.
The NEAB's director of key stage 3 marking recalled all the scripts and has taken personal charge of the inquiry.
The governors say the credibility of KS3 standard assessment tasks is seriously threatened: "If effective quality control measures are not in place, then confidence in KS3 testing will be seriously undermined," they said.