There are a lot of questions here, including basics like:
1) How big is the facility? A building? A factory? A city block?
2) What are the potential threats to it? Just the local gangers, or are professionals going to come sniffing?
3) What are the consequences of a security breach? Inconvenience? Catastrophe?
4) How long does security need to be provided? A week? A year?
If you want a number, one approach would be to start with the overall project size from the government's standpoint and make the overall security budget 16-20% of that.
Then, since a lot of this isn't well-defined, you're going to have to decide how much things cost, like IC, the hired help, etc. including the cost-to-quality ratio for each. Presumably the players will enjoy this process as part of their legwork; otherwise don't do it.
The end result will be be the budget surplus - which could grow or shrink depending on how effectively they negotiate with the subcontractors - which represents the players' profits/earnings. This might be a fun risk/reward equation as they attempt to cut corners and pocket as much as possible for themselves, just like all good Johnsons do.
Come to think of it, maybe the better approach is to start with how much profit you want them to earn, then back into the other figures from there. You, the GM, want the players to have ¥500k at their disposal. Their estimated profit margin is 10%, so let's assume that the overall security budget is ¥5MM, and the overall project is ¥25MM. That still gives them the fun of spending the ¥4.5MM while doing their best to optimize the budget.
You can tweak any of those figures (profit, profit margin, security budget, overall budget) to your liking. Whatever makes the most sense in your world.