The governing body was accused by a number of clergy earlier this week of failing to uphold the teaching of the Bible after it voted to bring about liturgies for welcoming transgender people and to ban gay conversion therapy.
Bishop of Norwich, Rt Rev Graham James wrote in The Daily Telegraph to respond to Bishop Michael Nazir Ali and others that said in the same publication that the decisions at the recent General Synod reflect "failures to uphold the teaching of the Bible".
Rt Rev James said: "The threefold sources of authority in the Church of England are scripture, tradition and reason, with scripture as the foundation. Nothing agreed at the recent synod undermines that.
"The synod voted against conversion therapy, which purports to make gay people straight. It did not seek to prevent prayer or accredited counselling for people uncomfortable with their sexuality".
Bishop Nazir Ali and more than 20 other prominent figures in the CofE warned of a growing schism between members who affirm the Bible and those who have "capitulated to secular values".
Their letter to The Daily Telegraph argued that there are "now effectively two opposed expressions of Anglicanism in this country".
The signatories also said that recent events at the General Synod have caused many Anglicans "great concern".
Rt Rev James also defended Synod's decision to ask the bishops to consider authorising liturgies to welcome transgender people.
He said: "This was prompted by stories of those who have felt rejected by the Church, and out of a biblical compassion for those who are frequently marginalised.
Earlier this year, the General Synod held discussions on a controversial report concerning sexuality which backed traditional marriage but also called for "maximum freedom" for homosexual people.
This month, the Synod supported a call for the House of Bishops to consider endorsing "gender transition".