Catholic Church-run health facilities in the country are no longer offering artificial contraceptives ever since last month.
The Catholic Church has about 115 health centres and nine hospitals in the country.
The move poses questions to family planning programme, whereby a married couple is advised to give birth to not more than three children.
Speaking to Sunday Times, Monsignor Philip Rukamba, the Bishop of Butare Diocese and President of the Episcopal Conference of Rwanda, said that the Church considers artificial contraceptive methods are not good and requests Catholics not to use them.
He said the birth control syringe, pills and other artificial contraceptive methods have many side effects.
He said the Church accepts the existence of family planning and that it was possible, but through natural methods, noting that CARITAS Rwanda, a Catholic Church based charity, offers such services in all the dioceses in the country.
"The church encourages use of 'natural' contraceptive methods. The system starts from knowing the fertility period of a woman and also [consists] of respect between a husband and a wife so that they cannot give birth to children they do not wish," he said.
The Bishop noted that the Church had agreed with the Government to ban artificial contraceptive methods in all the health centres and hospitals of the Catholic Church about five years ago.
He said subsequently, the Ministry of Health (MoH) established secondary health posts - near the hospitals or health centres owned by the Catholic Church - in a bid to receive people who seek artificial contraceptive methods to control births. He said these health posts often work with the public health facilities.
Bishop Rukamba noted that what made the issue come up again was that some people who the centres seeking artificial contraceptives facilities did not get them and started complaining.
He added that new local leaders also tended not to understand the Catholic Church's stand on those methods.
Letters sent to health facilities owned by the Catholic Churches and district officials about two months ago, intended to remind them that the church agreed with the government on that matter.
"Therefore, I wrote them a new letter that they would be showing to all people requesting those services to explain why they do not offer them," he said.
According to SexualityandU.ca, a Canadian sexual health public education initiative website, Natural Family Planning (NFP) typically refers to natural birth control that is taught and practiced within a religious framework, most commonly Catholic centred organisations.
It does not support the use of barrier methods, emergency contraception, or abortion.
Monsignor Rukamba noted that: "The Bible tells us that God told us to give birth and proliferate, but did not tell us how many one has to give birth to. Giving birth should also go in tandem with availability of resources".
What is the way forward?
The Vice Mayor for Social Affairs in Gisagara District, Clemance Gasengayire told Sunday Times that there were two hospitals in the District, with one - Gakoma Hospital - being the property of the Catholic Church and 14 health centers, of which six are owned by the Church.
"In fact before, they (the Catholic Church) prohibited the provision of the artificial contraceptive services from within their health facilities, and therefore, we decided to set up secondary health posts. But that time, the health worker in charge of PF (family planning) at the church-run health centre used to offer such services outside that health centre (at the secondary health post)," she said.
"But currently, the letter we received stated that the health worker, who is an employee of the church, should not offer that [family planning] service effective July 1," she said.
She said the district has a target to retain and increase the number of people in the family planning programme, noting that in the last financial year 2015/2016, family planning had 55.1% and that they want to reach 57% in 2016/2017.
According to the Rwanda Demographic and Health Survey 2014-15 (2014-15 RDHS), artificial contraceptive methods are the most used to control births.
Currently, survey shows 53% of married women in Rwanda use contraception, 48% of whom use modern methods and 6% depend on traditional methods of contraception.
Among married women, the survey states, injections, implants, and the pill are the most popular. Use of any method of family planning has greatly increased from 17% in 2005 to 53% in 2014.
Modern method contraceptive use has increased nearly five times from 10% in 2005 to 48% in 2014-15, the report shows.
Fertility has decreased from 6.2 births per woman in 1992 to 4.2 birth per woman in 2014, a decrease of 2.0 births per woman.