The containers were ordered a few weeks ago and Ministry spokesman Karl-Heinz Grundböck confirmed in an interview with Ö1 radio that Containex was commissioned to provide the order for a fee of €12 million - with no opportunity for other companies to bid for the contract.
He said that this was within the law as the containers were urgently needed to house the growing number of refugees requesting asylum in Austria, and Containex was able to provide them quickly.
The Greens party has said it will table a parliamentary question as to whether the government has paid over the odds for the containers, and should have put the contract out to tender.
It's estimated that the government will pay €17,000 for each container home, which competitors say is almost twice the amount such a container costs when purchased for use as a weekend home, Ö1 reported, quoting unnamed competitors of Containex.
However, Grundböck told the Austria Press Agency that the €12 million contract included 700 container homes which would be delivered immediately, and a further 500 to be supplied later. He said that the price also included the installation and assembly of the homes, and that some containers were already occupied by refugees.
In a written response, Containex said that the contract also included laying foundations for the container homes, installing power and fitting additional roofs or making changes to the interiors.
Containex is based in Wiener Neudorf, employs around 300 people and is part of the Walter Group. It is Europe's largest manufacturer of container housing, and has also provided containers for France, Switzerland and Germany this year - countries which are also struggling to house refugees.
Refugee support groups say that container housing is not ideal, as what is meant to be a short-term solution can end up becoming permanent, with people living in temporary housing for years.