This is the subjunctive, which takes the same form as the bare infinitive.
It is more common in American English than in British English and is a relatively formal usage. In British English, the form "should" + bare infinitive is more often used. Occasionally, the indicative form is used instead (which is only distinct in the third-person singular), though not everyone would consider this correct.
The subjunctive is often used when describing requests, commands, suggestions or requirements:
- He requested that she take notes.
- I ordered that he lay down his arms.
- It is necessary that you be there.
So yes, you can say "it is intended that the plan qualify as ..." or "it is intended that the plan should qualify as ...". To my ear, the indicative "qualifies" would sound odd here.
A slightly less formal re-wording would use the infinitive: "it is intended for the plan to qualify as ...". In many other sentences, the more common wording likewise uses infinitives ("he asked her to take notes", "I ordered him to lay down his arms").
See also: https://en.oxforddictionaries.com/grammar/when-to-use-the-subjunctive