Q: Are there passages in the Bible which would uphold pastors and missionaries when they refuse to baptize babies and young children?”
A: Your question is a difficult one to answer hypothetically, not knowing what reason might be stated by the clergyman for refusal. There are, of course, numerous passages in Scripture which place the responsibility for having children baptized and brought up in the saving truth of Christ with the parents or guardians. Passages that speak to this responsibility are the following: Col. 3:20, 21; Prov. 1:8, 9; Gen. 17:23, 25; Eph. 6:4; Prov. 13:24; and Mark 10:13-16. Even if one parent or guardian consents to having the infant baptized, this ought to suffice for the administrant to proceed. The Lutheran pastor will gladly baptize all infants for whom he can get a proper guarantee that they will be brought up in the nurture and admonition of the Lord,” (The Lutheran Pastor, p. 298).
Since the Bible speaks of baptism as “a washing of regeneration and renewing of the Holy Ghost” (Titus 3:5), we trust that God brings immediate blessing through this Sacrament. Unable to read the heart of a child, we cannot tell whether baptism has worked faith in each instance, but we dare not doubt the regenerative power to do so. Paul wrote in Galatians 3:27, “For all of you who were baptized into Christ have clothed yourselves with Christ.” Baptism, as with any means of grace, can be rejected. Yet, in cases of baptized infants who give no sign of rejection, we assume that their baptism has been effective. Along with this, goes the prayer that the regenerative infant will receive continual training in the Word of God—the vehicle the Holy Spirit uses to keep that faith alive. For this reason, it is important for the pastor or missionary to speak with the child’s parents about the need for having the child instructed in the Word and to obtain assurances in this regard. Otherwise, the child may soon be led to despise the very baptism which brought new life to its soul.
In a practical way, two instances come to mind when a pastor or missionary might decide against baptizing an infant. One would be in the case of outright verbal opposition by both parents to the child having further instruction in God’s Word. The other would be in the case of someone “slyly” arranging the baptism without the consent of those responsible for the child’s upbringing.
At the same time, however, “the pastor should not categorically refuse to baptize a child if the parents do not promise that the child will in the future receive biblical instruction,” (The Shepherd Under Christ, p. 73) [emphasis mine]. After all, baptism—as was stated—brings immediate blessing. And when opportunities come, we need to make use of them (Gal. 6:10)—even when there is only a small indication that the child will be under the Word in his/her upbringing. The entire church also has a role to play in attempting to nurture the child spiritually.
To my knowledge, there are no passages in Scripture which would automatically support refusal to baptize an infant once a request has been forthcoming.