There are 2 ways to get Negative Mass/Fuel for the ship.
If you are on Sythyrya go to the Scrap shop and purchase them.
If you are NOT on Sythyrya, go to the bridge of the ship and perform a Galactic Union Mission entitled "Distress Signal". This has a 100% chance of getting a Negative Mass/Fuel for your ship.
It may take a while for that "Distress Signal" mission to appear in the list of Galactic Union Missions that you can perform.
If you have some saved Negative Mass/Fuel you can wait until the ship has ZERO Negative Mass/Fuel remaining to power the ship.
Do this via going to the ships Engine and clicking on Recharge the Core.
So always ensure you have saved plenty of Negative Mass/Fuel for your ship, you don't want to have to restart your game or revert back to a previous "Saved" backup in the game.