Mattsson heads the Expressen daily newspaper, and in the fall of 2010 he gave one of the newspaper's reporters permission to buy a pistol in Malmö in southern Sweden.
Authorization was granted in connection with the reporter's efforts to show how easy it was to obtain a firearm in Sweden.
"If journalists can't work under cover, investigative journalism is robbed of one of its most important opportunities for unveiling wrongdoings," said Mattsson to newspaper Dagens Nyheter (DN).
The reporter has also been charged, as has the head of news on duty that day.
Purchasing the pistol was intended to show readers how simple it is to get hold of illegal weapons in Malmö, as part of the newspaper's reporting on the hunt for the serial shooter then on the loose in Sweden's third largest city.
It took Expressen five hours to get hold of their weapon, a 7.65 millimetre Crvena Zastava pistol.
Editor-in-chief Mattsson was the one who decided that the weapon be bought, and then immediately turned over to the police.
According to a statement made by the police, "Malmö is flooded with weapons".
"The idea of Expressen not conducting active journalism at that point is completely foreign to me. If politicians and police are claiming things, and calling for changes to the laws, it's our journalistic duty to investigate if what they say is true," said Mattsson to DN.
Prosecutor Jörgen Larsson wrote in his report that he found the charges justified from the public's perspective.
"This is a situation that Expressen has created on its own. The defense is built on the line that it was journalistically defensible to buy this weapon, and that's why I think there's a public interest in clarifying whether this is criminal or not," said Larsson to newspaper Dagens Media.
Thomas Mattsson, the reporter and the head of news have all denied the crimes.
"There was absolutely no intent," said Mattsson to news agency TT.