Goshi Hosono, PM Kan's assistant cum minister in charge of the Fukushima nuclear accident cum paymaster for the nuclear disaster compensation scheme that will help electric power companies who run nuke plants by capping the compensation, thinks that by putting the Nuclear Safety Agency under the Ministry of the Environment, the influence from, and collusion with, the nuclear industry will be lessened. (Hosono himself is a proponent of nuclear power, by the way.)
Well, what about safety? How would that be promoted, by putting the Agency under a ministry that has near-zero expertise and knowledge in nuclear power?
Remember also that it is the Ministry of the Environment who is very eager to raise the radiation limit of radioactive debris from 8,000 becquerels/kg to 100,000 becquerels/kg so that the debris can be burned at any facility anywhere in Japan and buried.
From Mainichi Shinbun (8/11/2011):
東京電力福島第１原発の事故を受け、原子力規制体制を抜本的に見直す新機関「原子力安全庁（仮称）」が、環境省の外局として設置されることが１１日決まった。原発を推進する経済産業省に安全規制官庁が属する長年のゆがみが解消される一方、霞が関では規模が小さな環境省の実行力や調整力には未知数の部分もある。
It was decided on August 11 that a new agency, Nuclear Safety Agency (temporary name) will be set up under the Ministry of the Environment. For a very long time, the regulatory agency for nuclear power, the Nuclear and Industrial Safety Agency, has been under the Ministry of Economy, Trade and Industry which has promoted nuclear power. That awkward situation of having the regulator and the promoter of nuclear power in the same ministry will be dissolved by moving the agency to the Ministry of the Environment. However, the Ministry of the Environment is one of the smaller ministries, and it is unknown whether the ministry can exert any effective leadership in nuclear regulation.
民主党の決定を受け、環境省には「心情的には反原発の職員が多い」「省内に原子力の専門家はほとんどいない」など戸惑いが広がった。環境省の職員は１２５８人（今年度）、予算規模も約２０００億円にすぎない。原子力安全庁には、経産省原子力安全・保安院や内閣府原子力安全委員会などから約５００人規模で加わるとみられ、「原子力ムラという独特の体質の集団でもあり、一つの組織として融合するには、１０年単位で時間がかかる。組織のバランスが崩れるのではないか」と心配する声があがる。
Upon hearing the decision by the Democratic Party of Japan (the ruling party), officials in the Ministry of the Environment are puzzled - "There are many here who are anti-nuke at heart", "We have hardly any experts in nuclear power". There are 1,258 personnel at the ministry, with the budget of only 200 billion yen [US$2.6 billion]. The Nuclear Safety Agency, which is to be newly created, will be staffed with 500 personnel from the METI's Nuclear and Industrial Safety Agency and the Nuclear Safety Commission under the Cabinet Office. There are those who voice concerns: "The Agency will continue to have the "Nuclear Village" mentality. It may take decades for the two organizations to effectively merge. We are afraid the balance of power within the ministry will be disturbed."
環境省はこれまで規制官庁として、公害問題などで「他省庁に嫌われる政府内野党の役割を果たしてきた」（幹部）自負を持つが、人員面、予算面から政府内の立場が強いとはいえず、他省庁との折衝で妥協を余儀なくされる場面も多かった。
The Ministry of the Environment prides itself in "acting as the opposition within the government" (according to senior officials of the ministry) in dealing with problems like pollution. However, it is not in a strong position within the government in terms of personnel and budget, and has often been forced to compromise in negotiation with the other more powerful ministries.
また、現在は原発の専門家がほとんどいないうえ、大事件や事故発生時の緊急対応の経験が少ないことも弱みだ。
Also, the ministry has hardly any nuclear expert as of now, and they don't have experience in emergency response during a big accident.
The Mainichi article quotes a Tokyo University professor (in government administration) who says the Ministry of the Environment is not really detached from the nuclear power interest groups, because it has promoted the nuclear power as environmentally friendly, clean energy to counter the "global warming".