PNG is mostly intended for web and small images, icons, etc, while PDF is generally the standard for printing. Also, forget about pixels when doing print work. Read this for a detailed explanation of how formats work.
This should be discussed with the company going to produce the actual banners, since each printer has different ways of looking at this, depending on their machines, workflow, etc. While most printers will probably prefer to print PDF's, some could require a JPG or TIF or EPS format.
When exporting a PDF for print, make sure you include crop and bleed marks, also something you need to discuss with the printing company.
About the actual size, you should be fine if you already have the canvas set to 3x1 meters, or half-size at 1.5x0.5 meters should also be fine. If the artwork is 100% vectors it should be easy to adjust this later in the process.