Method for the modified atmosphere packaging of products placed in trays, using an apparatus of the type comprising a downwardly open upper housing containing the welding means and preferably also containing the means for cutting the barrier film for sealing the trays, and an upwardly open lower housing with a chamber having at least one seat for housing a tray which can be moved into and out of this seat, and comprising means for positioning a stretched portion of film between the two housings (1, 8) and above the trays, as well as means for bringing said housings towards each other to clamp between them the edges of the tray and said film above these edges, and also comprising means operating at the correct time to inject process gases into the tray to preserve the product placed in the tray, before the subsequent step of welding the film onto the edge of the tray and the subsequent cutting along the perimeter of the portion of film welded to the tray, wherein means are provided to operate in such a way that said housings (1, 8) form within them a main chamber delimited above by the film for covering the tray and below by the tray containing the product, and laterally by any suitable mechanical interface structure which surrounds the perimeter of said film and connects it to the perimeter of the upper edge of the tray, this interface structure being provided with holes and/or slots which are suitably distributed and located outside the perimeter of the tray and which communicate with said main chamber, one or more of these holes opening substantially in one portion or side of the tray and being connected to a first circuit (23, 24), while another one or more of said holes open(s) in at least one opposing portion or side of the tray and is/are connected to a second circuit characterized in that the second circuit is connected to the inner chambers of the two housings (1, 8), and in that means (18, 19, 20) are provided to operate in such a way that, at the correct time, air is extracted from the tray in a vacuum formation step, the vacuum formation step being prior to the process gas injection step and wherein in the vacuum formation step, both said first circuit and said second circuit are connected to vacuum forming means which are kept active for a sufficient time to eliminate 30-50% of the air from the inside of the tray and to operate in such a way that, in the next step or at the correct time, said first circuit is connected to means for supplying the process gases, while said second circuit is closed or remains connected to the vacuum means in such a way that the process gas flowing into one part of the tray through said first circuit (22, 24) forces the residual air in the tray to flow out from and/or towards at least one opposing part of the tray, through said second circuit (22', 17), the whole arrangement being such that the inner volume of the tray is simultaneously flushed and saturated, thus uniformly occupying, without the formation of vortices or reflux and therefore very rapidly and reliably, the whole extension of said main chamber comprising the film, the tray and the product, which is subsequently sealed using known steps and means of welding and final cutting of the film and also characterized by the fact that in the said interface structure supplementary openings and/or slots (22") are provided which are open in correspondence of the other two sides of the tray, the said supplemental openings being in communication with the internal chamber (9, 109) of the lower housing