"The provision of buses towards Austria was a one-off and there will be no more vehicles sent to refugees walking along the road" towards Vienna, Karoly Papp told a news conference, quoted by state news agency MTI.
Overnight and today morning around 90 buses brought several thousand migrants to Hungary's western border. Some 6,500 had crossed into Austria by early afternoon.
Austria allowed them to cross over and provided special buses and trains to take them to Vienna, Salzburg and into Germany - the chosen destination for all but a handful.
Today at least 500 people took part in another march from Keleti towards Austria, after around 800 migrants reportedly walked out of Hungary's second largest refugee camp outside the eastern city of Debrecen.
Police prevented them from joining the M1 motorway, directing them onto a national road. An AFP photographer at the scene said the migrants were begging police to "please send us buses".
Prime Minister Viktor Orban, who has taken a hard line against the migrants, warning against the arrival of so many Muslims from a "profoundly different culture", said today it was "unacceptable" for people to block motorways.