The schools - Monmouth, Caldicott and Chepstow comprehensives in Gwent - lie close to the border with England and draw pupils from both sides.
Each has been accused of breaking Welsh Office regulations by not providing Welsh on their time-tables. Ministers are now demanding an explanation.
A spokeswoman for the Welsh Office said: "We have written to the schools asking them for the facts. In Wales the law says schools must teach Welsh up to key stage 3."
Compulsory Welsh was introduced into schools in the principality as part of the 1988 Education Act. Schools in predominately English-speaking areas, like the three in Gwent, were given until 1992 to introduce compulsory Welsh. The alleged failure to do so has meant that pupils have been unable to sit GCSE in Welsh.
Gwent education authority is seeking an urgent meeting with the schools' governing bodies but the issue is unlikely to be resolved before the start of the new academic year.
David Hopkins, Gwent's assistant education director, said: "We are aware that there have been difficulties in a number of schools in recruiting staff in order to develop the curriculum to incorporate Welsh.
"The problem for Welsh schools is that they only get the same number of hours in the day as schools in England but they have got an additional subject to squeeze in.
"Many schools perceive that another subject is suffering at the expense of Welsh."
Chepstow and Monmouth comprehensives take a significant number of pupils from nearby Gloucestershire and Hereford and Worcester. At Monmouth it is estimated that 200 pupils come across from England.
Mr Hopkins said: "We are very mindful of that fact. If you start to impress Welsh on people coming from over the border you might start to lose pupils. "
John Huntley, the chair of Chepstow governors, said a relaxation of rules was needed: "We wanted dispensation because of the possibility that pupils may move to schools in England."
Bill Morris, Caldicott's chair of governors, said the school's budget was too tight to provide funding for teaching Welsh. He said: "This is something the Welsh Office should finance."
Difficulties in recruiting Welsh teachers are heightened in local education authorities like Gwent, where fewer than one in 30 people speak the language.
The Welsh Language Board, the quango charged with nurturing the language, has complained to the Government about the situation in Gwent.
Meirion Jones, the board's chief education officer, said: "It is laid down in the Act that the schools should be teaching Welsh. We'll be asking the Welsh Office further questions."
The three schools are believed to be the only ones in Wales that have not introduced Welsh language teaching at key stage 3.
A spokeswoman for the Welsh Office said they were awaiting a response from the governing bodies at Caldicot, Chepstow and Monmouth before deciding what action to take. Mr Hopkins, from Gwent, said: "We wish to talk with the governors at each of the schools concerned."