The measures, including store security, CCTV and internal anti-skimming devices, will be rolled out to 1,900 cash machine sites.
APACS estimates that £95m a year is stolen every year from consumer bank accounts by skimmers.
Tesco Personal Finance director of operations Duncan McKinnell said: "ATM networks across the country are being increasingly targeted by fraudsters. £3m is a worthwhile investment to protect our customers' cash.
"Customers used our ATMs more than 300 million times last year and we want every one of them to feel secure. We believe our investment, combined with our customers' vigilance, will help us stay one step ahead of the fraudsters."