The pipeline was discovered on the bed of the river Chu, which forms the border between the two countries.
They suspect thousands of litres of pure spirit have passed through it.
It is unclear how officials made the discovery, but a search is now on for the smugglers behind the pipeline.
Local media has reported that the pipeline was found just a few kilometres from a border checkpoint.
Correspondents say that Kazakhstan is one of the biggest grain producers in Central Asia and spirits are far cheaper there than in neighbouring countries.
Kazakhstan is also a recent member of a customs union – along with Russia and Belarus – which has made it far more expensive for neighbouring countries to import alcohol without paying hefty duties.
Border guards recently discovered a similar pipeline used to smuggle oil products, including petrol and diesel.
It was set up because Kazakhstan is also a big oil producer – and oil products are much cheaper there than in its neighbours.