Primaries have delivered on testing but secondaries have not, Lord Lindsay, a Scottish Office minister, told the Lords in the final stage of the Education (Scotland) Bill, which has received royal assent.
Confirming Commons amendments on national testing in the first two years of secondary school, Lord Lindsay said secondaries had been given an extra year to prepare. "That delay should have meant that secondary rates started at a decent level and rose swiftly. But the reality is that the rates of national testing in secondary schools are distressingly low."
He added: "For the latest available full-year period, testing rates in the three tested areas of reading, writing and mathematics were, respectively, 9 per cent, 5 per cent and 8 per cent. Several of the former education authorities reported testing rates in each of the subject areas of under 5 per cent.
"These rates are unacceptably low and they have not appreciably improved over the past 18 months."
Lord Lindsay said a significant number of schools were asking for testing materials, yet few were conforming to the guidelines agreed by ministers with the education authorities in 1993.
"All the while, parents wait to see results of their children's progress, as measured against nationally set standards," he stated.
Lord Carmichael, Labour's frontbencher, expressed a number of reservations about national testing and the tight timetable for schools to introduce it in August next year.
"The question arises of the stress on children given the tight time-scale and the fact that the tests are likely to be marked by an outside body. The implication is that primary pupils teachers are unable to assess pupils properly and that a basic entry assessment is needed to offset that deficiency," he said.
Lord Carmichael added: "Primary school staff will try to prepare pupils for the test in S1. There are fears of a narrowing of the curriculum. I am not trying to reduce the importance of the subjects themselves, but too narrow a focus on reading, writing and mathematics at this stage is not the best way."
He concluded: "I do not like Education Bills, or any sort of Bills, to fail one after the other. But I am sure there will need to be yet another Education Bill sometime in the not too distant future."
Besides compulsory testing, the Act establishes the new qualifications authority, reforms procedures for school boards, modifies placing request rules for pupils moving into an area, blocks opting out to avoid school closures, and ensures councils consider safety when making transport arrangements for individual pupils.
The most controversial section of the legislation paves the way for nursery vouchers.