But it has been seen by others as an opportunity to begin gradual change.
Berdymukhamedov has called for limited reforms, including allowing access to the internet, reorganisation of the education system and getting more doctors and hospitals after two decades of authoritarian rule by Niyazov.
Limited internet access
Under Niyazov, internet access was only available only to officials, journalists and some other organisations.
When Berdymukhamedov was health minister in 2005, he was responsible for implementing Niyazov's order to close all hospitals outside the capital, Ashgabat, and fire about 15,000 doctors.
Five lesser-known candidates from the sole legal political party were Berdymukhamedov's only opponents in Turkmenistan's first multi-candidate leadership election.
The People's Assembly - the country's highest representative body which includes hundreds of parliamentarians, ministers, regional leaders and elders - applaused the new president after he was sworn in.
Berdymukhamedov promised "to respect all the laws and the constitution, to work for the good of the people and the development of our country while following the way traced by Saparmurat Turkmenbashi".
Niyazov kept the country largely isolated for 21 years, styling himself as Turkmenbashi, or leader of the Turkmen.
Joao Soares, a Portuguese parliamentarian said on Sunday the vote was "absolutely not free and fair".
"But ... the fact that they are at least trying to do something that resembles a free election is a step forward."
Soares led a group of European MPs from the Organisation for Security and Cooperation's Parliamentary Assembly, and experts from the OSCE's human rights arm.
Two UN officials and some foreign diplomats also visited polling stations.
Human-rights groups and a leading international think-tank have cautioned that Berdymukhamedov is a relative unknown and his prospective government should show progress on human rights and reform before being rewarded with trade and aid.
The exiled opposition, many of whom are former ministers who fell out of Niyazov's favour, have accused Western nations of accepting the new leadership in Turkmenistan in pursuit of gas.
Turkmenistan has major natural gas reserves and could play an important role in plans to create an energy corridor from Central Asia to Europe via the Caspian Sea.
Russia relies heavily on discounted Turkmen gas imports to be able to meet its own export obligations to Western Europe.