The 28-year-old Ivory Coast international recently joined the Bundesliga side from Dutch club Ajax.
Dortmund said Haller "complained that he felt unwell after training on Monday" and, following medical tests, "a testicular tumor" was discovered.
Further examinations will now take place "over the coming days".
"This news today came as a shock to Sebastien Haller and everyone else," said Dortmund sporting director Sebastian Kehl.
"The entire BVB family hopes that Sebastien makes a full recovery as soon as possible and that we can give him a hug again soon.
"We'll do everything in our power to ensure that he receives the best possible treatment."