The union is to conduct a survey of schools funded by PPP and the private finance initiative (PFI) to discover the extent of the difficulties teachers face. Members will receive survey forms this month.
News of the survey comes as East Lothian announced that work is to restart next month on its PPP projects after construction firm Balfour Beatty bailed out the council and its financial partners. Ballast, the previous contractor, went bust, leaving a trail of debt and work unfinished.
One EIS concern is that PPP schools are too small with ministers signalling cuts to a maximum of 20 pupils in English and mathematics classes in the first two years of secondary. Some headteachers believe it may prove difficult to meet the demand for space.
Ronnie Smith, the union's general secretary, said that teachers in all parts of Scotland had been raising their concerns.
"Some problems are likely to be teething difficulties but some are likely to be longer term, for example, when facilities are not adequate for modern education purposes," Mr Smith said. "We also receive reports of modern purpose-built schools which are a vast improvement on leaky, rundown schools, long past their sell-by date.
"What we need now is a clear picture of both of the benefits and the problems which PPP schools can bring."
The union, along with others, retains a principled objection to PPP financing but accepts it can bring new schools more quickly.
The survey will cover the extent to which staff are consulted about facilities and how new or refurbished buildings can benefit teaching and learning. It will look at the number and size of classrooms, whether there are enough computers and issues around the adequacy of sports facilities.
Some teachers in Glasgow, for example, have warned that school swimming has suffered after pools were removed from the city's new secondaries.
Other aspects of the survey cover community use of schools and the relationship with the private providers that own and run the buildings.
Mr Smith said: "Today, the majority of problems relating to PPP schools are to do with the initial stages of moving into them, whether new or refurbished. These have to do with work still going on on site and related problems of noise pollution, dust and general disruption.
"In some cases, essential facilities in the school are not yet ready, such as libraries and other support materials essential for learning. Some pupils may face disadvantage when it comes to Scottish Qualification Authority examinations the following summer."
Mr Smith said the most pressing long-term issue was the upkeep and maintenance of PPP-run schools. "Private investors expect a return on their investment. If this is not seen as forthcoming, there are real dangers of what could happen to schools, which, at the moment, may look modern, new, safe and well-equipped," he said.
The survey's findings will be unveiled in April.