The effect of magnetic Ni and non-magnetic Zn impurities on superconducting transition temperature Tc in RuSr2R(Cu1−x(Ni, Zn)x)2O8 with R = Gd or Eu (Ni- and Zn-substituted Ru1212Gd(Eu)) was extensively studied. It is found that the suppression rate dTc/dx of RuSr2R(Cu1−x(Ni, Zn)x)2O8 is comparable to that of underdoped YBa2(Cu1−x(Ni, Zn)x)3O7−δ. The suppression of superconductivity in Ni-substituted Ru1212Eu samples is more significant than that in Zn-substituted ones, indicative of Ni being a more effective pair-breaker than Zn. In strong contrast, the magnetic Ni impurity atoms have a weaker effect on superconductivity than non-magnetic Zn atoms in Ru1212Gd, similar to what was observed in the high-Tc cuprates. These intriguing findings strongly suggest that the impurity-induced local disturbance of the 3d-spin correlation at Cu sites around Ni/Zn is distinctly different between Ru1212Gd and Ru1212Eu.