Bakiyev said the changes were to make the government more effective, but the opposition dismissed his moves as merely a grab at greater power.
Bakiyev is exploiting the reforms to cement his hold on power, Felix Kulov, a former prime minister, told the AFP news agency.
"It must be recognised that President Kurmanbek Bakiyev has greatly strengthened the power of the executive branch," he said.
"Since the establishment of independence, no similarly massive reforms have occurred."
But Mars Sariyev, an independent political analyst, told AFP that the moves were necessary to reform a "broken political system".
"It is possible to say that this unprecedented updating of the state management system is a courageous step," Sariyev said.
"If the president had put off the reforms for one or two years, then he would likely not have been able to affect such cardinal reforms with corresponding consequences by the end of his term."
Bakiyev won a second five-year term as president in July, but critics dismissed the election as rigged.
Monitors also described the vote as a "disappointment" and said it had failed to meet international standards.
Bakiyev was first elected in 2005, in a poll seen as free and fair by Western observers.
But since then the opposition has accused him of becoming increasingly repressive.