However, Kenkyukai faced problems one after another: the leadership struggle with Sawakai led by Tosuke HIRATA, another aide to YAMAGATA; withdrawal from the faction by the group led by Takatomi SENGE (in 1898) because of the opposition to the policy of absolute adhesion to the faction decision called 'Ketsugi kosoku shugi' under which all members had to follow the faction decision and were not allowed to support bills proposed by non-kenkyukai members without resolution by the faction, and those who broke the rules were expelled from the faction; and the stifle over the expulsion of a founding member, Masayasu Hotta after his entry into the first SAIONJI Cabinet (Seiyu-kai Party) followed by the withdrawal from the faction by members who opposed to the expulsion (in 1909).
ところが、清浦と同じく山県側近であった平田東助の茶話会（幸倶楽部とも）との主導権争いが始まり、内部では清浦によって形成された他会派にはない「決議拘束主義」と呼ばれる絶対的な会派拘束（会の決議には全員従う事・会の決議なくして研究会以外の議員提出の法案・決議などに賛成してはならない事、これらに反したものは除名する事）に対する反発より千家尊福派（主として男爵議員）の離脱（1898年）、創設メンバーである堀田正養の第1次西園寺内閣（政友会）への入閣と除名騒動とこれに反発した議員の脱会（1909年）などが発生した。