While officially confirmed as a canonical installment in the series, Portable Ops is considered a spin-off game, despite the relative importance of events that occur in its storyline. As such, the events of Portable Ops receive notably little mention in official Konami press, compared with other installments in the series, which has caused some amount of confusion among the fanbase.
Portable Ops is not mentioned in the documentary Metal Gear Saga Vol. 2, though it is included in the timeline at the end, and footage is seen during the credits. The timeline on the Metal Gear Solid 4 website also mentions Portable Ops. Likewise, Metal Gear Solid 4 itself frequently used stills from Portable Ops in its cutscenes (made especially apparent with the EVA and Liquid Ocelot montage cutscenes in Acts 3 and 5, respectively) alongside the rest of the games, and artwork for Portable Ops by Noriyoshi Ohrai likewise briefly appeared in the church in Act 3 alongside other artwork by Ohrai, and some plot elements from Portable Ops were also referred to subtly (a notable example being the revelation that Zero founded the Patriots).
Despite being its chronological predecessor, the events of Portable Ops are barely acknowledged in Metal Gear Solid: Peace Walker, though it was included in the Metal Gear website's timeline during Peace Walker's development. In addition, Kazuhira Miller says the line, "Now we can leave that crap at San Hieronymo behind," early in the Prologue mission of Peace Walker. This caused debate among fans, as to whether Miller was referring to the events of Portable Ops, in which he was not involved, or whether this statement debunked the events of that game altogether.
Unlike Peace Walker, Portable Ops did not receive an HD update, and thus was not included in any version of the Metal Gear Solid: HD Collection or the upcoming Metal Gear Solid: The Legacy Collection. Kojima later revealed on Twitter that the reason why Portable Ops will not be included in The Legacy Collection is due to the fact that he was not directly involved in the game's development. As such, it remains confined to the PSP platform, while all other canonical games are playable on the PlayStation 3 console (the MSX2 games are included in Metal Gear Solid 3). It is also the only canonical Metal Gear Solid title to not be asked as a favorite of the player, in the upload screen of Metal Gear Solid: Snake Eater 3D. The MSX2 games are similarly not asked as a favorite of the player in the same game.
In a podcast for Kojima Productions, Kojima stated via his translator that Portable Ops is canon. The official website, likewise, kept Portable Ops on the Saga timeline, although only as a brief footnote. The MSX2 games were given similar treatment on the same website. In addition, the Japanese Konami site had a 25th Anniversary timeline that omitted Portable Ops, although it should be noted that in a previous timeline hosted by the Konami site, occurring around the time Peace Walker was in development, had erroneously omitted the MSX2 games from the timeline, leading to the possibility of it being an error on part of the Konami staff, and in either case, Portable Ops was still included in the chronology section of the site. In addition, two levels from Portable Ops were also included in Peace Walker's online mode, specifically the Silo Entrance and the Soviet Patrol Base.