But the result of a Downing Street inquiry was denounced as "utter whitewash" by Conservative MP Anne Main.
The St Albans MP complained after learning that the 2011 lunch included discussion of a controversial planning application by a developer in her constituency.
Cabinet Secretary Sir Jeremy Heywood said that Ms Villiers had assured him the lunch with the company's chief lobbyist Simon Hoare was "a personal engagement with a long-standing friend", and that she did not take any action as a result or pass on the content of their discussion to officials or ministers in the transport or communities departments.
He said: "This is a position that has been supported by accounts from both departments and I have absolutely no reason to doubt these accounts."
And he added: "Having considered this matter in full, I believe that both departments acted properly in respect of the planning appeal and that there is no evidence that decisions were affected by lobbying on behalf of Helioslough or other parties."
Ms Main said: "My constituents could be forgiven for thinking this was a whitewash.
"I am very angry and deeply disappointed by the scant response. My letter of complaint was four pages long and the response was less than one and a half.
She added that her allegations concerning 7.1 of the Ministerial Code which states that ministers must make sure that no conflict arises, or be reasonably perceived to arise, between their public duties and their private interests, were not addressed.
Developers Helioslough's application for planning permission for a £400 million international rail freight exchange on 300 acres of green belt between St Albans, in Hertfordshire, and London has faced stiff opposition from residents.
The MP added: "I am not stopping until I have got to the bottom of this."