It follows the company posting a £300m pre-tax loss for 2016 earlier this year. At its annual general meeting last week, the publisher also reported digital audience growth of 11% year on year.
The restructure means that Jeff Moriarty, chief digital and product officer, will oversee the new digital and publishing arm, as well as group marketing and events.
Moriarty said that the restructure will help the company "preserve our print readership for decades to come".
Richard Thomson, publishing director, has been named group publishing director and will expand his remit to include leading the publishing strategy for i and The Scotsman.
Meanwhile, Paul Napier has become publishing director. He has been running the publisher’s digital news brands as director of digital newsbrand products.
Nigel Leigh, director for commercial products and events, is now senior director for commercial products and events.
Johnston Press said there will not be any redundancies as part of the restructure.
Moriarty said: "This cross-platform approach in publishing acknowledges that our audiences will continue to move towards digital and yet we must preserve our print readership for decades to come.
"We must have an integrated approach - and get the print/digital balance right in each market - in order to continue to grow audiences, optimise revenues and ensure a vibrant mix of news brands that reach national, regional and local customers."