It comes after a report, published by Working Families, suggested thousands of fathers are suffering burn-out as they try to juggle work and family life.
Mark Chester, founder of Who Let the Dads Out, said: "I think this is a real challenge for the church. We need to do a lot more to support fathers - both Christians and non-Christians.
"Over 50% of churches run a parent and toddler group, so that means over 50% of churches are every week reaching mothers and their children, predominantly. Less than 1% of churches support fathers and their children on a weekly basis.
"The signs are encouraging. Churches are picking up the need to reach out and support fathers and their children. But I think what's need is a culture change in churches."
Working Families' Modern Families Index also found the younger generation of fathers feel the most resentful towards their employers (42%, compared to 32% overall) and also represent the group that is least comfortable asking employers for working time limits.
It claims more than half of millennial fathers (58%) would not feel confident asking their employer about reducing their hours, working remotely or placing boundaries on responding to calls or emails.
Mr Chester believes this can spell danger for those wanting to lead their families spiritually: "Christian fathers might take up their responsibility at church with enthusiasm, and in the process could potentially be at risk of neglecting their families.
"The other way it can go is that Christian fathers don't get engaged with the church, don't get the support they need, and then being a father becomes a more lonely existence.
"Our children are our first mission field; they are the people God has given to us with direct responsibility. So as Christian fathers we need to be encouraged to see that, and supported in how we fulfil that responsibility. But also reaching out to non-Christian dads. Very few churches do that."
The traditional gender roles are changing, according to the Modern Families Index.
Sarah Jackson, Chief Executive of Working Families, said: "Younger parents are more likely to share care than the generations before them. But they're on shaky ground because working life hasn't caught up. Long and inflexible hours remain the norm with many parents telling us they work up to ten extra hours a week. If we want children to have the time with parents that they need, and for parents to give their best at work, employers need to tackle unrealistic and unmanageable workloads. Otherwise we're short-changing families and we're short-changing the economy."
Mark Chester echoed the call: "We need some understanding from employers. We need them to encourage flexible working, but also set an example by doing it themselves."