There were 4% more suspensions from England's secondary schools last year though apparently fewer expulsions, latest official figures show.
The trend over recent years
There were 343,840 suspensions of teenagers for things such as assault, abuse, bullying and disruption.
Education Minister Jim Knight said schools were using the "short, sharp shock" to nip problems in the bud.
The Liberal Democrats said it was suspicious that the figures did not count exclusions from academies.
Mr Knight said: "The rise in fixed period exclusions reflects the tough approach schools are taking to address bad behaviour."
The Department for Education and Skills statistics show parents lodged 1,060 appeals against the expulsion of their child, 3% down on the previous year.
Of the appeals heard, parents won almost a quarter (24.1%) - up almost three percentage points on the previous year.
Of those successful appeals, the panel ordered the reinstatement of the pupil in their old school in 56% of cases - up six percentage points.
Shadow schools minister Nick Gibb said it was "very disturbing" that heads were being overruled in this way.
"The cumbersome and long drawn out processes that follow exclusion can act as a deterrent to excluding disruptive children in the first place.
"We need to empower headteachers to enable them to impose good behaviour in their schools."
Head teachers' representatives also expressed concern.
The general secretary of the National Association of Head Teachers, Mick Brookes, said reinstating a pupil could create "havoc".
He said the message it sent was that disruption was acceptable.
In general the figures relate to incidents rather than numbers of pupils - with some pupils being excluded more than once.
There was a marked fall in exclusions from special schools
There were 9,170 permanent exclusions from primary, secondary and special schools.
That was 3% less than the previous year. But - with falling school rolls - the rate was unchanged at 0.12% of the school population or 12 pupils in every 10,000.
Boys were almost four times more likely than girls to be excluded.
Pupils with special educational needs were about eight times more likely to be excluded than those without.
The average suspension was for 3.5 days though in 13,120 cases it was for more than two weeks.
Officials are said to be checking the missing data on academies, which are independently run state schools.
A spokesman for the department confirmed that the annual data on exclusions have never included academies, although this has not been spelt out before.
In the previous year, 2004-05, there were said to have been about 102 permanent exclusions from the 14 academies that were open.
The next year another 10 academies opened.
Revealing the figures in a Parliamentary written answer, Mr Knight said they were high, relative to national averages.
He said this was because academies were "placing great emphasis on getting the basics right and improving behaviour in particular".
"Academies often inherit a large number of disruptive pupils and need to establish good behaviour in order to raise attainment.
"As the new ethos and behaviour policy are enforced in an academy's early days, the number of exclusions may rise, but it typically drops down as behaviour improves."
Liberal Democrat education spokeswoman Sarah Teather said the omission of the data was rather suspicious.
"Academies are supposed to replace failing schools in tough areas so by leaving them out the government will have seriously altered the overall picture of school discipline.
"There are also indications that some academies use excessive exclusions and suspensions as a form of back door selection.
"To squash such rumours the government should publish the data immediately to show that it is not the case."