Recently, enterprises have paid attention to permissioned blockchain (BC), where business transactions among inter-authorized organizations (forming a consortium) can automatically be executed on the basis of a distributed consensus protocol, and applications of BC have expanded as permissioned BC has adopted the features of the smart contract (SC), which is programmable user-defined business logic deployed in BC and executed with the consensus protocol. A single BC-based system will be built across multiple management domains (e.g., the data centers of each organization) having different operational policies (e.g., operational procedures, timing, etc.); although establishing system management and operations over BC-based systems (e.g., SC installation for updates) will be important for production uses, such multi-domain formation will trigger a problem in that executing system operations over BC-based systems will become time-consuming and costly due to the difficulty in unifying and/or adjusting operational policies. Toward solving the problem, we propose an operations execution method for BC-based systems; the primary idea is to define operations as a smart contract so that unified and synchronized cross-organizational operations can be executed effectively by using BC-native features. For the recent BC architecture in which participating nodes have different types of roles, we designed the proposed method as a hybrid architecture characterized with in-BC consensus establishment and execution status management and out-BC operations execution for all types of nodes operated by agents that listen to triggered events including operational instructions defined in SCs. We implemented a prototype with Hyperledger Fabric v1.2.0. A cost estimation with the prototype shows that the total yearly cost of SC installation operations could be reduced by 74 percent compared with a manual method.