Kohl, 83, told British daily The Times that he respected the honesty of Thatcher, who died of a stroke on Monday aged 87, but added her stubbornness had blocked progress in the 1980s towards achieving a more deeply integrated political union.
"It is true – Margaret Thatcher was difficult, just as our relationship was difficult," Kohl told the paper.
"Unlike with other leaders in Europe and the world, and despite the best efforts of both sides, Margaret and I simply never managed to build a trusting and warm relationship.
"[She] wanted Europe, but a different Europe from that wanted by most of her European colleagues and me. From our point of view, this antagonism characterises British policy on Europe to this day," he added.
Despite their professional differences, Kohl paid tribute to "an admirable woman" and a "great prime minster."
"I also never once found her to be dishonest," he added. "For all that and for her love of freedom I always appreciated her. I will always honour the memory of Margaret Thatcher."
He explained that ill health would prevent him from attending next Wednesday's London funeral.
Thatcher famously secured a landmark budget rebate from the European Union in 1984, which rankles French and German counterparts to this day, especially with current British premier David Cameron leading so far successful efforts to cut back European Commission head Jose Manuel Barroso's €1.0 trillion 2014-20 plan.
Thatcher was eventually forced out from within her own Conservative party, a move that could be traced back to an infamous "No, No, No" speech in which she accused Berlin and Paris of building a "fortress Europe", and refused to surrender sterling for a nascent euro.