I think that the general concensus in that the storyline in general is true ie, he was sent to a penal colony for murder and subsequently escaped from different penal colonies etc but many of the smaller tales seem to be either too implausible or claimed by someone else.
Since Charriere cooperated with the film, which tells a rather different story to the book, I think one has to accept that he is rather flexible concerning accuracy. However, that does not mean that the whole thing is fiction.
I think that it is generally accepted that Charriere intended to write about the experiences of many inmates of the penal colony but was persuaded to write in the first person by his translator. I remember reading that Charriere made no secret of this and even regretted it when in conversation with others after the publication and he became a world-wide celebrity.
In 1938 there was a similar book by Rene Belbenoit called Dry Guillotine. He did escape and reached France and then was recaptured and returned to the colony. By a strange quirk of fate he was returned on the same shipment as Charriere. I don't know if the two ever met. Belbenoit also wrote an indictment of the colony entitled Hell on trial. Anyone interested in Papillon is recommended to hunt out these two books which confirm much of the sheer horror of the colony. Just out of interest, the publication of these books were helpful in the eventual closure of the prisons. Belbenoit himself eventually ended his days as a shoe-salesman in the USA - California from memory.
The Belneboit books will be difficult or expensive to obtain. However, The Convict by Felix Milani published in 1978 is relatively easy to obtain. Milani relates his experiences which parallel those of Charriere to some extent. Milani mentions Charriere and appears to have known him in the colony.
When The Convict was first published, La Stampa mentioned in their review-
"If Charriere is the astute Homer of the deeds of convicts, Milani is the genuine Ulysses"
Just out of interest, Dry Guillotine was also issued under the title "I escaped from Devil's Island" and was filmed as a quickie to cash in on the publicity for Papillion. Some reviewers refer to it as grade Z but it is still worthwhile hunting out as it was produced by Roger Corman and directed by William Witney. There are reviews on the IMDb site.