The comments come just days after his club marched into the Champions League semi-finals with a last-gasp win over Qatar-owned Malaga. Another Qatar-backed club, Paris St Germain, narrowly lost out on a last-four spot to Barcelona.
"This [big cash injections] is neither sportsmanlike nor fair and our core business is still sport," Watzke told the Handelsblatt newspaper on Friday. "We do not need to come with respect and fair play if this is not reflected on all levels."
Malaga are owned by Sheikh Abdullah Al Thani, a member of the Qatar royal family.
The club, however, has been banned from future European competitions over outstanding payments to other teams, staff and tax authorities. They have appealed the ban.
France's PSG have spent more than 200 million euros in transfers since the Qatari fund QSI bought the club in June 2011.
"I have the feeling that some sheikhs looked at the flight schedules and then picked a pretty metropolis because that is where the connections to the Gulf region are the best. But that is not how it works," he said.
Watzke has been instrumental in guiding Borussia Dortmund from the brink of bankruptcy in 2005 to a period of financial boom, fuelled by two consecutive Bundesliga titles and a German Cup in the past two seasons.
With roughly 80,000 spectators per game, Dortmund have the second-highest average attendance figure across Europe, behind Barcelona.
"There needs to develop a brand, a trigger force. That is something the gentlemen from the Arab region need to learn," Watzke added.
